rs923828

Positions:

• chr12-57621711-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_120450.1(LOC101927583):​n.193C>T 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: LOC101927583 NR_120450.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.84

Genes affected

(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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101927583	NR_120450.1	n.193C>T		non_coding_transcript_exon_variant	1/4
SLC26A10P	NR_166679.1	n.1271G>A		non_coding_transcript_exon_variant	4/16
SLC26A10P	NR_166678.1	n.1271G>A		non_coding_transcript_exon_variant	4/14

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000440686.5	n.449G>A		non_coding_transcript_exon_variant	4/16	2
SLC26A10P	ENST00000665594.1	n.808G>A		non_coding_transcript_exon_variant	5/18

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

GnomAD3 exomes AF: 0.346 AC: 77879 AN: 224952 Hom.: 14642 AF XY: 0.352 AC XY: 43205 AN XY: 122826

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 SAS exome AF: 0.246

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

Gnomad4 AFR exome AF: 0.162

Gnomad4 AMR exome AF: 0.271

Gnomad4 ASJ exome AF: 0.534

Gnomad4 EAS exome AF: 0.189

Gnomad4 SAS exome AF: 0.252

Gnomad4 FIN exome AF: 0.338

Gnomad4 NFE exome AF: 0.426

Gnomad4 OTH exome AF: 0.399

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

Gnomad4 AFR AF: 0.173

Gnomad4 AMR AF: 0.350

Gnomad4 ASJ AF: 0.545

Gnomad4 EAS AF: 0.234

Gnomad4 SAS AF: 0.241

Gnomad4 FIN AF: 0.322

Gnomad4 NFE AF: 0.433

Gnomad4 OTH AF: 0.409

Alfa AF: 0.424 Hom.: 33409

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 v4.3

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
MutationTaster	Benign	0.74	P;P
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

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

Publications

LitVar

Other links and lift over

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