rs3762344

Variant names:

• chr1-206895327-G-A
• rs3762344
• ENST00000830172.1:n.177+302C>T

Variant summary

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

The ENST00000830172.1(ENSG00000307982):​n.177+302C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.465 in 152,010 control chromosomes in the GnomAD database, including 16,947 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 0.47 (16947 hom., cov: 32)
• Consequence: ENSG00000307982 ENST00000830172.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.287
• Publications: 11 publications found

Genes affected

ENSG00000307982 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.554 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372879	XR_007066835.1	n.125+667C>T		intron_variant	Intron 1 of 1
LOC105372879	XR_007066836.1	n.125+667C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000307982	ENST00000830172.1	n.177+302C>T		intron_variant	Intron 1 of 1
ENSG00000307982	ENST00000830173.1	n.68+302C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70636 AN: 151892 Hom.: 16930 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.223

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.456

Gnomad OTH AF: 0.489

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

GnomAD4 genome AF: 0.465 AC: 70708 AN: 152010 Hom.: 16947 Cov.: 32 AF XY: 0.456 AC XY: 33916 AN XY: 74302

African (AFR) AF: 0.561 AC: 23229 AN: 41442

American (AMR) AF: 0.461 AC: 7049 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1630 AN: 3464

East Asian (EAS) AF: 0.222 AC: 1149 AN: 5174

South Asian (SAS) AF: 0.234 AC: 1128 AN: 4816

European-Finnish (FIN) AF: 0.375 AC: 3963 AN: 10564

Middle Eastern (MID) AF: 0.514 AC: 151 AN: 294

European-Non Finnish (NFE) AF: 0.456 AC: 30980 AN: 67958

Other (OTH) AF: 0.492 AC: 1034 AN: 2100

Alfa AF: 0.462 Hom.: 63167

Bravo AF: 0.477

Asia WGS AF: 0.277 AC: 964 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.6
DANN	Benign	0.40
PhyloP100		0.29

Splicing

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

Other links and lift over

dbSNP: rs3762344; hg19: chr1-207068672;