chr1-41468937-A-C

Variant names:

• chr1-41468937-A-C
• rs2095289

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 0.404 in 151,640 control chromosomes in the GnomAD database, including 12,739 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 0.40 (12739 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.24
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.452 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: 0.404 AC: 61256 AN: 151534 Hom.: 12732 Cov.: 31

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.368

Gnomad AMR AF: 0.461

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.393

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

GnomAD4 genome AF: 0.404 AC: 61300 AN: 151640 Hom.: 12739 Cov.: 31 AF XY: 0.412 AC XY: 30497 AN XY: 74110

African (AFR) AF: 0.317 AC: 13067 AN: 41280

American (AMR) AF: 0.461 AC: 7028 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1264 AN: 3466

East Asian (EAS) AF: 0.451 AC: 2314 AN: 5134

South Asian (SAS) AF: 0.452 AC: 2171 AN: 4808

European-Finnish (FIN) AF: 0.516 AC: 5428 AN: 10522

Middle Eastern (MID) AF: 0.305 AC: 89 AN: 292

European-Non Finnish (NFE) AF: 0.424 AC: 28774 AN: 67870

Other (OTH) AF: 0.393 AC: 831 AN: 2112

Alfa AF: 0.422 Hom.: 1730

Bravo AF: 0.392

Asia WGS AF: 0.456 AC: 1583 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.7
DANN	Benign	0.81
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs2095289; hg19: chr1-41934608;