rs2056169

chr5-71763885-A-Cchr5-71763885-A-Gchr5-71763885-A-T

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 0.322 in 152,048 control chromosomes in the GnomAD database, including 9,656 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 0.32 (9656 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.68

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.556 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.322 AC: 48849 AN: 151930 Hom.: 9628 Cov.: 32

Gnomad AFR AF: 0.561

Gnomad AMI AF: 0.325

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.240

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.318

Gnomad FIN AF: 0.238

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.322 AC: 48937 AN: 152048 Hom.: 9656 Cov.: 32 AF XY: 0.321 AC XY: 23886 AN XY: 74326

Gnomad4 AFR AF: 0.562

Gnomad4 AMR AF: 0.292

Gnomad4 ASJ AF: 0.240

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.317

Gnomad4 FIN AF: 0.238

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.291

Alfa AF: 0.202 Hom.: 1845

Bravo AF: 0.339

Asia WGS AF: 0.349 AC: 1212 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.035
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2056169; hg19: chr5-71059712; COSMIC: COSV50461023;