rs3891636

Variant names:

• chr5-131103398-T-C
• rs3891636

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.302 in 151,830 control chromosomes in the GnomAD database, including 8,198 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 0.30 (8198 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.273

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.5 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: 0.302 AC: 45783 AN: 151710 Hom.: 8178 Cov.: 31

Gnomad AFR AF: 0.505

Gnomad AMI AF: 0.0570

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.221

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.302 AC: 45836 AN: 151830 Hom.: 8198 Cov.: 31 AF XY: 0.300 AC XY: 22224 AN XY: 74190

Gnomad4 AFR AF: 0.505

Gnomad4 AMR AF: 0.217

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.268

Gnomad4 NFE AF: 0.221

Gnomad4 OTH AF: 0.274

Alfa AF: 0.226 Hom.: 7125

Bravo AF: 0.301

Asia WGS AF: 0.292 AC: 1016 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.9
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3891636; hg19: chr5-130439091;