chr1-96041174-A-C

Variant names:

• chr1-96041174-A-C
• rs1144305

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 0.712 in 152,066 control chromosomes in the GnomAD database, including 38,850 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 0.71 (38850 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.42
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.748 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: 0.712 AC: 108178 AN: 151948 Hom.: 38839 Cov.: 32

Gnomad AFR AF: 0.626

Gnomad AMI AF: 0.808

Gnomad AMR AF: 0.734

Gnomad ASJ AF: 0.807

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.768

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.719

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

GnomAD4 genome AF: 0.712 AC: 108234 AN: 152066 Hom.: 38850 Cov.: 32 AF XY: 0.709 AC XY: 52701 AN XY: 74306

African (AFR) AF: 0.626 AC: 25950 AN: 41468

American (AMR) AF: 0.734 AC: 11214 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.807 AC: 2800 AN: 3468

East Asian (EAS) AF: 0.664 AC: 3418 AN: 5148

South Asian (SAS) AF: 0.754 AC: 3640 AN: 4830

European-Finnish (FIN) AF: 0.706 AC: 7461 AN: 10562

Middle Eastern (MID) AF: 0.771 AC: 225 AN: 292

European-Non Finnish (NFE) AF: 0.754 AC: 51272 AN: 68006

Other (OTH) AF: 0.720 AC: 1519 AN: 2110

Alfa AF: 0.718 Hom.: 6889

Bravo AF: 0.709

Asia WGS AF: 0.700 AC: 2437 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.77
DANN	Benign	0.80
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs1144305; hg19: chr1-96506730; COSMIC: COSV59975292;