rs10515077

Variant names:

• chr5-68317973-A-C
• rs10515077

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0551 AC: 2291 AN: 41578

American (AMR) AF: 0.155 AC: 2369 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.114 AC: 394 AN: 3470

East Asian (EAS) AF: 0.172 AC: 891 AN: 5170

South Asian (SAS) AF: 0.0487 AC: 235 AN: 4824

European-Finnish (FIN) AF: 0.0695 AC: 737 AN: 10606

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0858 AC: 5837 AN: 68004

Other (OTH) AF: 0.0885 AC: 187 AN: 2114

Alfa AF: 0.0912 Hom.: 1779

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
PhyloP100		1.5

Splicing

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

Other links and lift over

dbSNP: rs10515077; hg19: chr5-67613801;