1-65690338-G-T

Variant names:

• chr1-65690338-G-T
• rs2211651

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 0.434 in 151,922 control chromosomes in the GnomAD database, including 14,971 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 0.43 (14971 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.60
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.846 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: 0.433 AC: 65806 AN: 151804 Hom.: 14949 Cov.: 32

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.470

Gnomad ASJ AF: 0.374

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.468

Gnomad FIN AF: 0.492

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.434 AC: 65884 AN: 151922 Hom.: 14971 Cov.: 32 AF XY: 0.442 AC XY: 32808 AN XY: 74230

African (AFR) AF: 0.442 AC: 18291 AN: 41418

American (AMR) AF: 0.470 AC: 7168 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.374 AC: 1299 AN: 3470

East Asian (EAS) AF: 0.867 AC: 4466 AN: 5152

South Asian (SAS) AF: 0.466 AC: 2243 AN: 4810

European-Finnish (FIN) AF: 0.492 AC: 5181 AN: 10524

Middle Eastern (MID) AF: 0.364 AC: 107 AN: 294

European-Non Finnish (NFE) AF: 0.382 AC: 25945 AN: 67978

Other (OTH) AF: 0.420 AC: 885 AN: 2108

Alfa AF: 0.387 Hom.: 20426

Bravo AF: 0.432

Asia WGS AF: 0.621 AC: 2155 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.12
DANN	Benign	0.75
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs2211651; hg19: chr1-66156021; COSMIC: COSV59950623;