rs2347061

Variant names:

• chr4-43535660-G-A
• rs2347061

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 0.884 in 152,144 control chromosomes in the GnomAD database, including 59,754 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 0.88 (59754 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.688
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.905 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: 0.884 AC: 134427 AN: 152028 Hom.: 59700 Cov.: 32

Gnomad AFR AF: 0.892

Gnomad AMI AF: 0.841

Gnomad AMR AF: 0.790

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.778

Gnomad FIN AF: 0.963

Gnomad MID AF: 0.883

Gnomad NFE AF: 0.911

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.884 AC: 134538 AN: 152144 Hom.: 59754 Cov.: 32 AF XY: 0.879 AC XY: 65384 AN XY: 74372

African (AFR) AF: 0.892 AC: 37068 AN: 41540

American (AMR) AF: 0.790 AC: 12058 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.875 AC: 3035 AN: 3470

East Asian (EAS) AF: 0.699 AC: 3605 AN: 5158

South Asian (SAS) AF: 0.779 AC: 3748 AN: 4814

European-Finnish (FIN) AF: 0.963 AC: 10212 AN: 10606

Middle Eastern (MID) AF: 0.891 AC: 262 AN: 294

European-Non Finnish (NFE) AF: 0.911 AC: 61942 AN: 67974

Other (OTH) AF: 0.873 AC: 1843 AN: 2110

Alfa AF: 0.906 Hom.: 8084

Bravo AF: 0.869

Asia WGS AF: 0.748 AC: 2598 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.7
DANN	Benign	0.61
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs2347061; hg19: chr4-43537677;