rs316736

Variant names:

• chr5-41645937-G-A
• rs316736

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 0.114 in 152,098 control chromosomes in the GnomAD database, including 1,482 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 (1482 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.229 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: 0.114 AC: 17322 AN: 151980 Hom.: 1468 Cov.: 32

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.0362

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0651

Gnomad EAS AF: 0.0331

Gnomad SAS AF: 0.130

Gnomad FIN AF: 0.0619

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0545

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.114 AC: 17379 AN: 152098 Hom.: 1482 Cov.: 32 AF XY: 0.114 AC XY: 8484 AN XY: 74344

African (AFR) AF: 0.233 AC: 9654 AN: 41444

American (AMR) AF: 0.133 AC: 2037 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0651 AC: 226 AN: 3472

East Asian (EAS) AF: 0.0332 AC: 172 AN: 5182

South Asian (SAS) AF: 0.130 AC: 627 AN: 4822

European-Finnish (FIN) AF: 0.0619 AC: 655 AN: 10582

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0545 AC: 3705 AN: 68002

Other (OTH) AF: 0.119 AC: 252 AN: 2114

Alfa AF: 0.102 Hom.: 198

Bravo AF: 0.125

Asia WGS AF: 0.101 AC: 352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.4
DANN	Benign	0.77
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs316736; hg19: chr5-41646039;