4-62253163-A-G

Variant names:

• chr4-62253163-A-G
• rs10517556

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 0.175 in 152,114 control chromosomes in the GnomAD database, including 2,711 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 0.18 (2711 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.42
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.46 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: 0.175 AC: 26603 AN: 151996 Hom.: 2711 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.477

Gnomad SAS AF: 0.323

Gnomad FIN AF: 0.179

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.175 AC: 26623 AN: 152114 Hom.: 2711 Cov.: 32 AF XY: 0.180 AC XY: 13420 AN XY: 74352

African (AFR) AF: 0.114 AC: 4731 AN: 41532

American (AMR) AF: 0.209 AC: 3191 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.182 AC: 632 AN: 3470

East Asian (EAS) AF: 0.476 AC: 2447 AN: 5140

South Asian (SAS) AF: 0.324 AC: 1562 AN: 4822

European-Finnish (FIN) AF: 0.179 AC: 1896 AN: 10564

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.172 AC: 11721 AN: 67984

Other (OTH) AF: 0.161 AC: 340 AN: 2114

Alfa AF: 0.132 Hom.: 403

Bravo AF: 0.173

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	9.0
DANN	Benign	0.29
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs10517556; hg19: chr4-63118881;