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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268031		n.124300419G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

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 v4.3

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;