chr5-71716480-T-A

Variant names:

• chr5-71716480-T-A
• rs10515115

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 0.345 in 152,012 control chromosomes in the GnomAD database, including 9,365 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 0.34 (9365 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.982
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.386 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: 0.345 AC: 52388 AN: 151890 Hom.: 9362 Cov.: 32

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.371

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.481

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.345 AC: 52406 AN: 152012 Hom.: 9365 Cov.: 32 AF XY: 0.346 AC XY: 25688 AN XY: 74292

African (AFR) AF: 0.235 AC: 9736 AN: 41488

American (AMR) AF: 0.364 AC: 5561 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.481 AC: 1669 AN: 3468

East Asian (EAS) AF: 0.332 AC: 1714 AN: 5156

South Asian (SAS) AF: 0.341 AC: 1642 AN: 4812

European-Finnish (FIN) AF: 0.414 AC: 4370 AN: 10552

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26469 AN: 67934

Other (OTH) AF: 0.369 AC: 780 AN: 2114

Alfa AF: 0.158 Hom.: 1242

Bravo AF: 0.338

Asia WGS AF: 0.316 AC: 1100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	11
DANN	Benign	0.64
PhyloP100		0.98

Splicing

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

Other links and lift over

dbSNP: rs10515115; hg19: chr5-71012307;