12-57621711-G-A

Variant names:

• chr12-57621711-G-A
• rs923828
• ENST00000474359.7:n.*887G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000474359.7(ENSG00000287908):​n.*887G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 1,600,702 control chromosomes in the GnomAD database, including 128,355 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.34 (9660 hom., cov: 33)
  • Exomes 𝑓: 0.40 (118695 hom.)
• Consequence: ENSG00000287908 ENST00000474359.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.84
• Publications: 41 publications found

Genes affected

ENSG00000287908 (HGNC:):

SLC26A10P (HGNC:14470): (solute carrier family 26 member 10, pseudogene) Predicted to enable anion transmembrane transporter activity. Predicted to be involved in anion transport. Predicted to be active in basolateral plasma membrane. Predicted to be integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (MetaRNN=0.0037638843).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.429 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000474359.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101927583	NR_120450.1		n.193C>T		non_coding_transcript_exon	Exon 1 of 4
	SLC26A10P	NR_166678.1		n.1271G>A		non_coding_transcript_exon	Exon 4 of 14
	SLC26A10P	NR_166679.1		n.1271G>A		non_coding_transcript_exon	Exon 4 of 16

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287908	ENST00000474359.7	TSL:5	n.*887G>A		non_coding_transcript_exon	Exon 12 of 23	ENSP00000431994.2
	ENSG00000287908	ENST00000474359.7	TSL:5	n.*887G>A		3_prime_UTR	Exon 12 of 23	ENSP00000431994.2
	ENSG00000293429	ENST00000440686.5	TSL:2	n.449G>A		non_coding_transcript_exon	Exon 4 of 16

Frequencies

GnomAD3 genomes AF: 0.335 AC: 50999 AN: 152034 Hom.: 9666 Cov.: 33

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.356

Gnomad AMR AF: 0.350

Gnomad ASJ AF: 0.545

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.322

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.414

GnomAD2 exomes AF: 0.346 AC: 77879 AN: 224952 AF XY: 0.352

Gnomad AFR exome AF: 0.169

Gnomad AMR exome AF: 0.259

Gnomad ASJ exome AF: 0.539

Gnomad EAS exome AF: 0.231

Gnomad FIN exome AF: 0.326

Gnomad NFE exome AF: 0.431

Gnomad OTH exome AF: 0.406

GnomAD4 exome AF: 0.397 AC: 574607 AN: 1448550 Hom.: 118695 Cov.: 50 AF XY: 0.395 AC XY: 283864 AN XY: 719088

African (AFR) AF: 0.162 AC: 5396 AN: 33262

American (AMR) AF: 0.271 AC: 11753 AN: 43292

Ashkenazi Jewish (ASJ) AF: 0.534 AC: 13768 AN: 25804

East Asian (EAS) AF: 0.189 AC: 7386 AN: 39150

South Asian (SAS) AF: 0.252 AC: 21350 AN: 84612

European-Finnish (FIN) AF: 0.338 AC: 17546 AN: 51902

Middle Eastern (MID) AF: 0.526 AC: 2941 AN: 5590

European-Non Finnish (NFE) AF: 0.426 AC: 470633 AN: 1105208

Other (OTH) AF: 0.399 AC: 23834 AN: 59730

GnomAD4 genome AF: 0.335 AC: 50994 AN: 152152 Hom.: 9660 Cov.: 33 AF XY: 0.330 AC XY: 24548 AN XY: 74386

African (AFR) AF: 0.173 AC: 7171 AN: 41546

American (AMR) AF: 0.350 AC: 5347 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.545 AC: 1893 AN: 3472

East Asian (EAS) AF: 0.234 AC: 1207 AN: 5158

South Asian (SAS) AF: 0.241 AC: 1162 AN: 4826

European-Finnish (FIN) AF: 0.322 AC: 3410 AN: 10604

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29441 AN: 67936

Other (OTH) AF: 0.409 AC: 863 AN: 2108

Alfa AF: 0.409 Hom.: 43978

Bravo AF: 0.331

TwinsUK AF: 0.444 AC: 1647

ALSPAC AF: 0.431 AC: 1662

ESP6500AA AF: 0.186 AC: 818

ESP6500EA AF: 0.434 AC: 3729

ExAC AF: 0.331 AC: 39989

Asia WGS AF: 0.243 AC: 846 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.094
BayesDel_addAF	Benign	-0.42	T
BayesDel_noAF	Benign	-0.24
CADD	Benign	17
DANN	Uncertain	1.0
DEOGEN2	Benign	0.12	T
Eigen	Benign	0.13
Eigen_PC	Benign	0.15
FATHMM_MKL	Uncertain	0.83	D
LIST_S2	Benign	0.74	T
MetaRNN	Benign	0.0038	T
MetaSVM	Benign	-1.2	T
MutationAssessor	Uncertain	2.1	M
PhyloP100		1.8
PrimateAI	Benign	0.43	T
PROVEAN	Benign	-0.53	N
REVEL	Benign	0.29
Sift	Benign	0.39	T
Sift4G	Benign	0.33	T
Polyphen		0.73	P
Vest4		0.12
MPC		0.52
ClinPred		0.018	T
GERP RS		3.9
Varity_R		0.14
gMVP		0.29
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs923828; hg19: chr12-58015494; COSMIC: COSV54089315; COSMIC: COSV54089315;