rs10515077

Positions:

• chr5-68317973-A-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 0.0859 in 152,258 control chromosomes in the GnomAD database, including 703 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 0.086 (703 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.46

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0858 AC: 13052 AN: 152138 Hom.: 696 Cov.: 33

Gnomad AFR AF: 0.0552

Gnomad AMI AF: 0.121

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.114

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.0485

Gnomad FIN AF: 0.0695

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0859

Gnomad OTH AF: 0.0880

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

GnomAD4 genome AF: 0.0859 AC: 13080 AN: 152258 Hom.: 703 Cov.: 33 AF XY: 0.0875 AC XY: 6510 AN XY: 74430

Gnomad4 AFR AF: 0.0551

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.114

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.0487

Gnomad4 FIN AF: 0.0695

Gnomad4 NFE AF: 0.0858

Gnomad4 OTH AF: 0.0885

Alfa AF: 0.0921 Hom.: 1072

Bravo AF: 0.0968

Asia WGS AF: 0.0940 AC: 324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.7
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10515077; hg19: chr5-67613801;