1-67287670-T-C

Variant names:

• chr1-67287670-T-C
• rs1495966

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 152,084 control chromosomes in the GnomAD database, including 23,082 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 (23082 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.271
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.63 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: 0.547 AC: 83091 AN: 151966 Hom.: 23070 Cov.: 33

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.574

Gnomad EAS AF: 0.492

Gnomad SAS AF: 0.438

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.540

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

GnomAD4 genome AF: 0.547 AC: 83153 AN: 152084 Hom.: 23082 Cov.: 33 AF XY: 0.541 AC XY: 40249 AN XY: 74356

African (AFR) AF: 0.561 AC: 23243 AN: 41462

American (AMR) AF: 0.640 AC: 9786 AN: 15282

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

East Asian (EAS) AF: 0.492 AC: 2549 AN: 5182

South Asian (SAS) AF: 0.437 AC: 2108 AN: 4826

European-Finnish (FIN) AF: 0.411 AC: 4340 AN: 10568

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.549 AC: 37311 AN: 67988

Other (OTH) AF: 0.538 AC: 1133 AN: 2106

Alfa AF: 0.540 Hom.: 9409

Bravo AF: 0.566

Asia WGS AF: 0.490 AC: 1703 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.72
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs1495966; hg19: chr1-67753353; COSMIC: COSV59951653;