chr10-113678707-G-A

Variant names:

• chr10-113678707-G-A
• rs11196418

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 0.116 in 145,172 control chromosomes in the GnomAD database, including 1,203 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 0.12 (1203 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.22
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.116 AC: 16899 AN: 145058 Hom.: 1202 Cov.: 26

Gnomad AFR AF: 0.0407

Gnomad AMI AF: 0.0975

Gnomad AMR AF: 0.0689

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.113

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.116 AC: 16893 AN: 145172 Hom.: 1203 Cov.: 26 AF XY: 0.117 AC XY: 8273 AN XY: 70624

African (AFR) AF: 0.0405 AC: 1565 AN: 38628

American (AMR) AF: 0.0687 AC: 992 AN: 14440

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 599 AN: 3418

East Asian (EAS) AF: 0.101 AC: 478 AN: 4734

South Asian (SAS) AF: 0.204 AC: 922 AN: 4524

European-Finnish (FIN) AF: 0.159 AC: 1528 AN: 9590

Middle Eastern (MID) AF: 0.117 AC: 31 AN: 264

European-Non Finnish (NFE) AF: 0.157 AC: 10475 AN: 66668

Other (OTH) AF: 0.107 AC: 216 AN: 2014

Alfa AF: 0.110 Hom.: 632

Bravo AF: 0.102

Asia WGS AF: 0.119 AC: 412 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	3.5
DANN	Benign	0.62
PhyloP100		1.2
PromoterAI		-0.00040	Neutral

Splicing

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

Other links and lift over

dbSNP: rs11196418; hg19: chr10-115438466;