rs3912601

Variant names:

• chr3-73362536-C-T
• rs3912601
• ENST00000840257.1:n.79+45054C>T

Variant summary

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

The ENST00000840257.1(ENSG00000309320):​n.79+45054C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 152,038 control chromosomes in the GnomAD database, including 8,601 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 0.33 (8601 hom., cov: 32)
• Consequence: ENSG00000309320 ENST00000840257.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.984
• Publications: 2 publications found

Genes affected

ENSG00000309320 (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 (EAS) allele frequency at 95% confidence interval = 0.506 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
ENSG00000309320	ENST00000840257.1	n.79+45054C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.330 AC: 50191 AN: 151920 Hom.: 8589 Cov.: 32

Gnomad AFR AF: 0.369

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.289

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.286

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.330 AC: 50223 AN: 152038 Hom.: 8601 Cov.: 32 AF XY: 0.335 AC XY: 24879 AN XY: 74314

African (AFR) AF: 0.369 AC: 15277 AN: 41444

American (AMR) AF: 0.338 AC: 5162 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1384 AN: 3472

East Asian (EAS) AF: 0.523 AC: 2697 AN: 5158

South Asian (SAS) AF: 0.442 AC: 2128 AN: 4818

European-Finnish (FIN) AF: 0.289 AC: 3058 AN: 10574

Middle Eastern (MID) AF: 0.418 AC: 123 AN: 294

European-Non Finnish (NFE) AF: 0.286 AC: 19438 AN: 67976

Other (OTH) AF: 0.366 AC: 775 AN: 2116

Alfa AF: 0.307 Hom.: 32518

Bravo AF: 0.337

Asia WGS AF: 0.481 AC: 1674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.25
DANN	Benign	0.42
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs3912601; hg19: chr3-73411687;