chr3-124025816-T-A

Variant names:

• chr3-124025816-T-A
• rs12637456
• ENST00000801819.1:n.81-6443T>A

Variant summary

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

The ENST00000801819.1(ENSG00000304291):​n.81-6443T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.423 in 152,006 control chromosomes in the GnomAD database, including 15,995 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 0.42 (15995 hom., cov: 32)
• Consequence: ENSG00000304291 ENST00000801819.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.414
• Publications: 5 publications found

Genes affected

ENSG00000304291 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.701 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
ENSG00000304291	ENST00000801819.1	n.81-6443T>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.423 AC: 64181 AN: 151888 Hom.: 15959 Cov.: 32

Gnomad AFR AF: 0.708

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.295

Gnomad EAS AF: 0.480

Gnomad SAS AF: 0.381

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.283

Gnomad OTH AF: 0.410

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

GnomAD4 genome AF: 0.423 AC: 64263 AN: 152006 Hom.: 15995 Cov.: 32 AF XY: 0.424 AC XY: 31522 AN XY: 74296

African (AFR) AF: 0.708 AC: 29307 AN: 41410

American (AMR) AF: 0.365 AC: 5575 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.295 AC: 1025 AN: 3472

East Asian (EAS) AF: 0.480 AC: 2475 AN: 5158

South Asian (SAS) AF: 0.380 AC: 1822 AN: 4800

European-Finnish (FIN) AF: 0.336 AC: 3549 AN: 10578

Middle Eastern (MID) AF: 0.346 AC: 101 AN: 292

European-Non Finnish (NFE) AF: 0.283 AC: 19215 AN: 68004

Other (OTH) AF: 0.416 AC: 877 AN: 2106

Alfa AF: 0.170 Hom.: 284

Bravo AF: 0.440

Asia WGS AF: 0.471 AC: 1635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.17
DANN	Benign	0.52
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs12637456; hg19: chr3-123744663;