chr1-166581264-C-T

Variant names:

• chr1-166581264-C-T
• rs1372685

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 0.572 in 151,814 control chromosomes in the GnomAD database, including 24,943 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 0.57 (24943 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.53
• Publications: 2 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 (AFR) allele frequency at 95% confidence interval = 0.589 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: 0.572 AC: 86786 AN: 151696 Hom.: 24942 Cov.: 31

Gnomad AFR AF: 0.595

Gnomad AMI AF: 0.700

Gnomad AMR AF: 0.517

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.552

Gnomad SAS AF: 0.417

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.693

Gnomad NFE AF: 0.577

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.572 AC: 86832 AN: 151814 Hom.: 24943 Cov.: 31 AF XY: 0.568 AC XY: 42119 AN XY: 74184

African (AFR) AF: 0.595 AC: 24616 AN: 41388

American (AMR) AF: 0.516 AC: 7865 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 2388 AN: 3468

East Asian (EAS) AF: 0.553 AC: 2847 AN: 5152

South Asian (SAS) AF: 0.416 AC: 1992 AN: 4788

European-Finnish (FIN) AF: 0.552 AC: 5821 AN: 10536

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.577 AC: 39188 AN: 67924

Other (OTH) AF: 0.606 AC: 1279 AN: 2110

Alfa AF: 0.566 Hom.: 11058

Bravo AF: 0.572

Asia WGS AF: 0.482 AC: 1672 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.24
DANN	Benign	0.72
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1372685; hg19: chr1-166550501;