rs10040679

Positions:

• chr5-134517641-T-C

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 0.125 in 152,254 control chromosomes in the GnomAD database, including 1,249 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 0.12 (1249 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.108

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.156 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: 0.125 AC: 18984 AN: 152136 Hom.: 1251 Cov.: 32

Gnomad AFR AF: 0.111

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.113

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.134

Gnomad FIN AF: 0.0662

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.144

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

GnomAD4 genome AF: 0.125 AC: 18999 AN: 152254 Hom.: 1249 Cov.: 32 AF XY: 0.122 AC XY: 9088 AN XY: 74434

Gnomad4 AFR AF: 0.111

Gnomad4 AMR AF: 0.113

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.165

Gnomad4 SAS AF: 0.136

Gnomad4 FIN AF: 0.0662

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.143

Alfa AF: 0.136 Hom.: 1502

Bravo AF: 0.126

Asia WGS AF: 0.112 AC: 387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.6
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10040679; hg19: chr5-133853332;