1-65691047-C-T

Variant names:

• chr1-65691047-C-T
• rs2889195

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 0.419 in 151,752 control chromosomes in the GnomAD database, including 14,016 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 0.42 (14016 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.845 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: 0.418 AC: 63444 AN: 151632 Hom.: 14000 Cov.: 31

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.331

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.375

Gnomad EAS AF: 0.867

Gnomad SAS AF: 0.463

Gnomad FIN AF: 0.494

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.382

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.419 AC: 63512 AN: 151752 Hom.: 14016 Cov.: 31 AF XY: 0.428 AC XY: 31711 AN XY: 74142

African (AFR) AF: 0.390 AC: 16110 AN: 41360

American (AMR) AF: 0.462 AC: 7048 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.375 AC: 1301 AN: 3470

East Asian (EAS) AF: 0.867 AC: 4461 AN: 5148

South Asian (SAS) AF: 0.461 AC: 2218 AN: 4808

European-Finnish (FIN) AF: 0.494 AC: 5192 AN: 10518

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

European-Non Finnish (NFE) AF: 0.382 AC: 25909 AN: 67896

Other (OTH) AF: 0.410 AC: 865 AN: 2108

Alfa AF: 0.377 Hom.: 8582

Bravo AF: 0.414

Asia WGS AF: 0.546 AC: 1643 AN: 3018

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.51
DANN	Benign	0.50
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2889195; hg19: chr1-66156730; COSMIC: COSV59950633;