rs515781

Variant names:

• chr1-43069342-G-A
• rs515781

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 0.113 in 152,262 control chromosomes in the GnomAD database, including 1,593 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 0.11 (1593 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.60
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.498 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: 0.113 AC: 17176 AN: 152144 Hom.: 1590 Cov.: 32

Gnomad AFR AF: 0.0766

Gnomad AMI AF: 0.0791

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.0637

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.188

Gnomad FIN AF: 0.148

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0793

Gnomad OTH AF: 0.101

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

GnomAD4 genome AF: 0.113 AC: 17192 AN: 152262 Hom.: 1593 Cov.: 32 AF XY: 0.121 AC XY: 9038 AN XY: 74434

African (AFR) AF: 0.0766 AC: 3184 AN: 41564

American (AMR) AF: 0.193 AC: 2959 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0637 AC: 221 AN: 3470

East Asian (EAS) AF: 0.515 AC: 2653 AN: 5154

South Asian (SAS) AF: 0.187 AC: 905 AN: 4828

European-Finnish (FIN) AF: 0.148 AC: 1575 AN: 10610

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0793 AC: 5395 AN: 68012

Other (OTH) AF: 0.103 AC: 218 AN: 2114

Alfa AF: 0.0899 Hom.: 1424

Bravo AF: 0.116

Asia WGS AF: 0.300 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	10
DANN	Benign	0.53
PhyloP100		3.6

Splicing

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

Other links and lift over

dbSNP: rs515781; hg19: chr1-43535013;