chr5-93114943-A-G

Variant names:

• chr5-93114943-A-G
• rs959922

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 0.55 in 151,732 control chromosomes in the GnomAD database, including 24,041 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 0.55 (24041 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0350

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 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: 0.550 AC: 83317 AN: 151614 Hom.: 24000 Cov.: 31

Gnomad AFR AF: 0.693

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.602

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.530

Gnomad FIN AF: 0.518

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.460

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.550 AC: 83421 AN: 151732 Hom.: 24041 Cov.: 31 AF XY: 0.555 AC XY: 41115 AN XY: 74140

Gnomad4 AFR AF: 0.694

Gnomad4 AMR AF: 0.602

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.529

Gnomad4 FIN AF: 0.518

Gnomad4 NFE AF: 0.460

Gnomad4 OTH AF: 0.509

Alfa AF: 0.525 Hom.: 3698

Bravo AF: 0.566

Asia WGS AF: 0.661 AC: 2296 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	5.8
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs959922; hg19: chr5-92450649;