1-80268896-C-T

Variant names:

• chr1-80268896-C-T
• rs11162963

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 0.593 in 151,870 control chromosomes in the GnomAD database, including 27,262 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 0.59 (27262 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.243
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.662 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: 0.593 AC: 90000 AN: 151752 Hom.: 27248 Cov.: 31

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.672

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.458

Gnomad SAS AF: 0.444

Gnomad FIN AF: 0.683

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.593 AC: 90049 AN: 151870 Hom.: 27262 Cov.: 31 AF XY: 0.593 AC XY: 43984 AN XY: 74220

African (AFR) AF: 0.497 AC: 20584 AN: 41420

American (AMR) AF: 0.673 AC: 10244 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2201 AN: 3468

East Asian (EAS) AF: 0.458 AC: 2351 AN: 5132

South Asian (SAS) AF: 0.446 AC: 2149 AN: 4818

European-Finnish (FIN) AF: 0.683 AC: 7216 AN: 10562

Middle Eastern (MID) AF: 0.531 AC: 155 AN: 292

European-Non Finnish (NFE) AF: 0.640 AC: 43471 AN: 67934

Other (OTH) AF: 0.584 AC: 1231 AN: 2108

Alfa AF: 0.611 Hom.: 37937

Bravo AF: 0.590

Asia WGS AF: 0.434 AC: 1511 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.67
PhyloP100		-0.24

Splicing

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

Other links and lift over

dbSNP: rs11162963; hg19: chr1-80734581;