rs10885497

Variant names:

• chr10-113733170-C-G
• rs10885497

Your query was ambiguous. Multiple possible variants found:

• chr10-113733170-C-G
• chr10-113733170-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 0.138 in 152,168 control chromosomes in the GnomAD database, including 2,117 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 0.14 (2117 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.260
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.284 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: 0.138 AC: 21036 AN: 152050 Hom.: 2114 Cov.: 32

Gnomad AFR AF: 0.0317

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.0584

Gnomad SAS AF: 0.0680

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.138 AC: 21035 AN: 152168 Hom.: 2117 Cov.: 32 AF XY: 0.143 AC XY: 10614 AN XY: 74390

African (AFR) AF: 0.0316 AC: 1311 AN: 41536

American (AMR) AF: 0.291 AC: 4447 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.116 AC: 401 AN: 3470

East Asian (EAS) AF: 0.0582 AC: 301 AN: 5176

South Asian (SAS) AF: 0.0674 AC: 325 AN: 4820

European-Finnish (FIN) AF: 0.220 AC: 2327 AN: 10570

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.169 AC: 11459 AN: 67998

Other (OTH) AF: 0.130 AC: 274 AN: 2112

Alfa AF: 0.0734 Hom.: 103

Bravo AF: 0.142

Asia WGS AF: 0.0820 AC: 285 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	3.5
DANN	Benign	0.80
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs10885497; hg19: chr10-115492929;