rs10956170

Variant names:

• chr8-124300419-G-A
• rs10956170

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 0.235 in 151,912 control chromosomes in the GnomAD database, including 4,429 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 0.24 (4429 hom., cov: 31)
• Consequence: LOC112268031 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18
• Publications: 2 publications found

Genes affected

LOC112268031 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.277 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35684 AN: 151792 Hom.: 4427 Cov.: 31

Gnomad AFR AF: 0.282

Gnomad AMI AF: 0.361

Gnomad AMR AF: 0.179

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.131

Gnomad FIN AF: 0.149

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.234

Gnomad OTH AF: 0.264

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

GnomAD4 genome AF: 0.235 AC: 35700 AN: 151912 Hom.: 4429 Cov.: 31 AF XY: 0.229 AC XY: 16985 AN XY: 74254

African (AFR) AF: 0.282 AC: 11661 AN: 41394

American (AMR) AF: 0.178 AC: 2722 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1061 AN: 3468

East Asian (EAS) AF: 0.235 AC: 1210 AN: 5140

South Asian (SAS) AF: 0.131 AC: 629 AN: 4814

European-Finnish (FIN) AF: 0.149 AC: 1568 AN: 10548

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.234 AC: 15887 AN: 67966

Other (OTH) AF: 0.261 AC: 552 AN: 2112

Alfa AF: 0.239 Hom.: 19235

Bravo AF: 0.243

Asia WGS AF: 0.168 AC: 585 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.3
DANN	Benign	0.44
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs10956170; hg19: chr8-125312660;