2-35657673-T-C

Variant names:

• chr2-35657673-T-C
• rs1401224

Variant summary

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

The variant allele was found at a frequency of 0.469 in 151,942 control chromosomes in the GnomAD database, including 18,299 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 (18299 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.516
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.687 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

Frequencies

GnomAD3 genomes AF: 0.469 AC: 71266 AN: 151824 Hom.: 18268 Cov.: 32

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.379

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.446

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

GnomAD4 genome AF: 0.469 AC: 71331 AN: 151942 Hom.: 18299 Cov.: 32 AF XY: 0.466 AC XY: 34562 AN XY: 74246

African (AFR) AF: 0.693 AC: 28740 AN: 41456

American (AMR) AF: 0.402 AC: 6132 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1246 AN: 3468

East Asian (EAS) AF: 0.331 AC: 1708 AN: 5158

South Asian (SAS) AF: 0.378 AC: 1816 AN: 4808

European-Finnish (FIN) AF: 0.346 AC: 3645 AN: 10536

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26546 AN: 67960

Other (OTH) AF: 0.442 AC: 930 AN: 2104

Alfa AF: 0.303 Hom.: 808

Bravo AF: 0.480

Asia WGS AF: 0.388 AC: 1349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.65
DANN	Benign	0.31
PhyloP100		-0.52

Splicing

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

Other links and lift over

dbSNP: rs1401224; hg19: chr2-35882739;