rs3885668

Variant names:

• chr2-10038352-C-T
• rs3885668
• ENST00000837794.1:n.377-1380G>A

Variant summary

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

The ENST00000837794.1(ENSG00000260077):​n.377-1380G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.6 in 152,082 control chromosomes in the GnomAD database, including 27,873 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 0.60 (27873 hom., cov: 32)
• Consequence: ENSG00000260077 ENST00000837794.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.05
• Publications: 17 publications found

Genes affected

ENSG00000260077 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268412	XR_002959369.2	n.1357-26C>T		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000260077	ENST00000837794.1	n.377-1380G>A		intron_variant	Intron 3 of 4
ENSG00000260077	ENST00000837795.1	n.409+2177G>A		intron_variant	Intron 4 of 4
ENSG00000260077	ENST00000837796.1	n.410-1380G>A		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.600 AC: 91224 AN: 151964 Hom.: 27839 Cov.: 32

Gnomad AFR AF: 0.542

Gnomad AMI AF: 0.388

Gnomad AMR AF: 0.671

Gnomad ASJ AF: 0.593

Gnomad EAS AF: 0.842

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.745

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.600 AC: 91310 AN: 152082 Hom.: 27873 Cov.: 32 AF XY: 0.611 AC XY: 45422 AN XY: 74340

African (AFR) AF: 0.542 AC: 22491 AN: 41460

American (AMR) AF: 0.671 AC: 10261 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.593 AC: 2055 AN: 3466

East Asian (EAS) AF: 0.842 AC: 4351 AN: 5168

South Asian (SAS) AF: 0.687 AC: 3312 AN: 4822

European-Finnish (FIN) AF: 0.745 AC: 7889 AN: 10594

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39185 AN: 67966

Other (OTH) AF: 0.594 AC: 1255 AN: 2114

Alfa AF: 0.592 Hom.: 16645

Bravo AF: 0.591

Asia WGS AF: 0.740 AC: 2573 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.039
DANN	Benign	0.59
PhyloP100		-4.1

Splicing

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

Other links and lift over

dbSNP: rs3885668; hg19: chr2-10178479;