5-163620473-C-G

Variant names:

• chr5-163620473-C-G
• rs17062061

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 0.208 in 152,012 control chromosomes in the GnomAD database, including 4,051 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 0.21 (4051 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402
• 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 (AFR) allele frequency at 95% confidence interval = 0.359 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: 0.208 AC: 31542 AN: 151894 Hom.: 4048 Cov.: 32

Gnomad AFR AF: 0.364

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.144

Gnomad OTH AF: 0.208

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

GnomAD4 genome AF: 0.208 AC: 31583 AN: 152012 Hom.: 4051 Cov.: 32 AF XY: 0.204 AC XY: 15138 AN XY: 74334

African (AFR) AF: 0.364 AC: 15083 AN: 41430

American (AMR) AF: 0.160 AC: 2448 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 640 AN: 3462

East Asian (EAS) AF: 0.158 AC: 818 AN: 5174

South Asian (SAS) AF: 0.180 AC: 865 AN: 4816

European-Finnish (FIN) AF: 0.119 AC: 1261 AN: 10568

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.144 AC: 9816 AN: 67974

Other (OTH) AF: 0.207 AC: 438 AN: 2116

Alfa AF: 0.179 Hom.: 387

Bravo AF: 0.217

Asia WGS AF: 0.197 AC: 685 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	0.76
DANN	Benign	0.35
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs17062061; hg19: chr5-163047479;