chr12-28666573-G-A

Variant names:

• chr12-28666573-G-A
• rs951821
• ENST00000849941.1:n.46+31259C>T

Variant summary

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

The ENST00000849941.1(ENSG00000310456):​n.46+31259C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 151,710 control chromosomes in the GnomAD database, including 9,527 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 0.35 (9527 hom., cov: 31)
• Consequence: ENSG00000310456 ENST00000849941.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.19
• Publications: 6 publications found

Genes affected

ENSG00000310456 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.421 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310456	ENST00000849941.1	n.46+31259C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52473 AN: 151592 Hom.: 9530 Cov.: 31

Gnomad AFR AF: 0.426

Gnomad AMI AF: 0.307

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.432

Gnomad EAS AF: 0.108

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.398

Gnomad NFE AF: 0.337

Gnomad OTH AF: 0.334

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.346 AC: 52490 AN: 151710 Hom.: 9527 Cov.: 31 AF XY: 0.342 AC XY: 25379 AN XY: 74144

African (AFR) AF: 0.426 AC: 17644 AN: 41416

American (AMR) AF: 0.266 AC: 4047 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.432 AC: 1494 AN: 3462

East Asian (EAS) AF: 0.107 AC: 552 AN: 5136

South Asian (SAS) AF: 0.340 AC: 1637 AN: 4816

European-Finnish (FIN) AF: 0.303 AC: 3198 AN: 10550

Middle Eastern (MID) AF: 0.390 AC: 114 AN: 292

European-Non Finnish (NFE) AF: 0.337 AC: 22828 AN: 67778

Other (OTH) AF: 0.330 AC: 697 AN: 2114

Alfa AF: 0.342 Hom.: 5375

Bravo AF: 0.339

Asia WGS AF: 0.223 AC: 777 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.4
DANN	Benign	0.50
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs951821; hg19: chr12-28819506;