1-67287825-C-T

Variant names:

• chr1-67287825-C-T
• rs1495965

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 0.547 in 152,006 control chromosomes in the GnomAD database, including 23,066 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 0.55 (23066 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0120
• Publications: 93 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.629 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.547 AC: 83056 AN: 151888 Hom.: 23054 Cov.: 32

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.412

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.541

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

GnomAD4 genome AF: 0.547 AC: 83118 AN: 152006 Hom.: 23066 Cov.: 32 AF XY: 0.541 AC XY: 40220 AN XY: 74300

African (AFR) AF: 0.560 AC: 23217 AN: 41436

American (AMR) AF: 0.640 AC: 9772 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.574 AC: 1992 AN: 3468

East Asian (EAS) AF: 0.492 AC: 2547 AN: 5172

South Asian (SAS) AF: 0.437 AC: 2106 AN: 4818

European-Finnish (FIN) AF: 0.412 AC: 4352 AN: 10556

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.549 AC: 37307 AN: 67974

Other (OTH) AF: 0.539 AC: 1136 AN: 2108

Alfa AF: 0.551 Hom.: 72385

Bravo AF: 0.566

Asia WGS AF: 0.490 AC: 1706 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	2.1
DANN	Benign	0.36
PhyloP100		0.012

Splicing

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

Other links and lift over

dbSNP: rs1495965; hg19: chr1-67753508; COSMIC: COSV59951656;