1-43157474-A-G

Variant names:

• chr1-43157474-A-G
• rs674684

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 0.5 in 151,554 control chromosomes in the GnomAD database, including 20,288 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 0.50 (20288 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.500 AC: 75685 AN: 151440 Hom.: 20252 Cov.: 30

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.251

Gnomad AMR AF: 0.485

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.432

Gnomad SAS AF: 0.431

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.469

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

GnomAD4 genome AF: 0.500 AC: 75777 AN: 151554 Hom.: 20288 Cov.: 30 AF XY: 0.501 AC XY: 37118 AN XY: 74042

African (AFR) AF: 0.704 AC: 28998 AN: 41212

American (AMR) AF: 0.485 AC: 7391 AN: 15230

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1620 AN: 3470

East Asian (EAS) AF: 0.433 AC: 2229 AN: 5148

South Asian (SAS) AF: 0.431 AC: 2067 AN: 4800

European-Finnish (FIN) AF: 0.474 AC: 4971 AN: 10492

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27172 AN: 67898

Other (OTH) AF: 0.465 AC: 977 AN: 2100

Alfa AF: 0.446 Hom.: 5770

Bravo AF: 0.511

Asia WGS AF: 0.428 AC: 1488 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.9
DANN	Benign	0.30
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs674684; hg19: chr1-43623145;