rs10060762

Variant names:

• chr5-111166346-G-A
• rs10060762

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 0.314 in 152,026 control chromosomes in the GnomAD database, including 8,095 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 0.31 (8095 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.267
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 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: 0.314 AC: 47632 AN: 151908 Hom.: 8089 Cov.: 32

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.201

Gnomad SAS AF: 0.343

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.256

Gnomad OTH AF: 0.295

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

GnomAD4 genome AF: 0.314 AC: 47670 AN: 152026 Hom.: 8095 Cov.: 32 AF XY: 0.313 AC XY: 23267 AN XY: 74320

African (AFR) AF: 0.457 AC: 18935 AN: 41442

American (AMR) AF: 0.294 AC: 4489 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 786 AN: 3470

East Asian (EAS) AF: 0.201 AC: 1036 AN: 5166

South Asian (SAS) AF: 0.343 AC: 1653 AN: 4824

European-Finnish (FIN) AF: 0.235 AC: 2490 AN: 10582

Middle Eastern (MID) AF: 0.282 AC: 83 AN: 294

European-Non Finnish (NFE) AF: 0.256 AC: 17419 AN: 67960

Other (OTH) AF: 0.296 AC: 624 AN: 2110

Alfa AF: 0.269 Hom.: 9646

Bravo AF: 0.320

Asia WGS AF: 0.292 AC: 1014 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.70
DANN	Benign	0.67
PhyloP100		-0.27

Splicing

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

Other links and lift over

dbSNP: rs10060762; hg19: chr5-110502044;