chr5-177313243-A-G

Variant names:

• chr5-177313243-A-G
• rs11949767

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 0.726 in 984,646 control chromosomes in the GnomAD database, including 260,002 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 0.70 (37447 hom., cov: 31)
  • Exomes 𝑓: 0.73 (222555 hom.)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.729 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: 0.700 AC: 106104 AN: 151598 Hom.: 37442 Cov.: 31

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.737

Gnomad ASJ AF: 0.817

Gnomad EAS AF: 0.453

Gnomad SAS AF: 0.654

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.842

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.738

GnomAD4 exome AF: 0.730 AC: 608271 AN: 832934 Hom.: 222555 Cov.: 39 AF XY: 0.731 AC XY: 281157 AN XY: 384648

Gnomad4 AFR exome AF: 0.642

Gnomad4 AMR exome AF: 0.724

Gnomad4 ASJ exome AF: 0.819

Gnomad4 EAS exome AF: 0.438

Gnomad4 SAS exome AF: 0.694

Gnomad4 FIN exome AF: 0.696

Gnomad4 NFE exome AF: 0.734

Gnomad4 OTH exome AF: 0.706

GnomAD4 genome AF: 0.700 AC: 106156 AN: 151712 Hom.: 37447 Cov.: 31 AF XY: 0.697 AC XY: 51626 AN XY: 74098

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.737

Gnomad4 ASJ AF: 0.817

Gnomad4 EAS AF: 0.453

Gnomad4 SAS AF: 0.653

Gnomad4 FIN AF: 0.709

Gnomad4 NFE AF: 0.734

Gnomad4 OTH AF: 0.735

Alfa AF: 0.731 Hom.: 37463

Bravo AF: 0.700

Asia WGS AF: 0.538 AC: 1876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.26
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11949767; hg19: chr5-176740244;