rs10060710

Variant names:

• chr5-156853545-C-A
• rs10060710

Your query was ambiguous. Multiple possible variants found:

• chr5-156853545-C-A
• chr5-156853545-C-G
• chr5-156853545-C-T

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 0.0954 in 151,998 control chromosomes in the GnomAD database, including 757 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 0.095 (757 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.395
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.136 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.0951 AC: 14441 AN: 151880 Hom.: 747 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.166

Gnomad AMR AF: 0.0867

Gnomad ASJ AF: 0.0638

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0985

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0712

Gnomad OTH AF: 0.0752

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

GnomAD4 genome AF: 0.0954 AC: 14503 AN: 151998 Hom.: 757 Cov.: 32 AF XY: 0.0972 AC XY: 7220 AN XY: 74310

African (AFR) AF: 0.132 AC: 5489 AN: 41470

American (AMR) AF: 0.0875 AC: 1336 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0638 AC: 221 AN: 3466

East Asian (EAS) AF: 0.110 AC: 572 AN: 5188

South Asian (SAS) AF: 0.145 AC: 698 AN: 4820

European-Finnish (FIN) AF: 0.0985 AC: 1042 AN: 10578

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0712 AC: 4832 AN: 67892

Other (OTH) AF: 0.0739 AC: 156 AN: 2110

Alfa AF: 0.0703 Hom.: 470

Bravo AF: 0.0949

Asia WGS AF: 0.125 AC: 435 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.4
DANN	Benign	0.64
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs10060710; hg19: chr5-156280556;