10-111072236-C-A

Variant names:

• chr10-111072236-C-A
• rs11195417

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 0.159 in 152,102 control chromosomes in the GnomAD database, including 2,552 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 0.16 (2552 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0340
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.29 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.159 AC: 24224 AN: 151984 Hom.: 2551 Cov.: 31

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.0947

Gnomad ASJ AF: 0.0600

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.0870

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.108

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.159 AC: 24241 AN: 152102 Hom.: 2552 Cov.: 31 AF XY: 0.157 AC XY: 11659 AN XY: 74372

African (AFR) AF: 0.295 AC: 12211 AN: 41456

American (AMR) AF: 0.0946 AC: 1447 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0600 AC: 208 AN: 3466

East Asian (EAS) AF: 0.190 AC: 979 AN: 5158

South Asian (SAS) AF: 0.154 AC: 742 AN: 4810

European-Finnish (FIN) AF: 0.0870 AC: 922 AN: 10600

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.108 AC: 7343 AN: 68000

Other (OTH) AF: 0.137 AC: 289 AN: 2112

Alfa AF: 0.126 Hom.: 4139

Bravo AF: 0.164

Asia WGS AF: 0.175 AC: 608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	12
DANN	Benign	0.73
PhyloP100		-0.034

Splicing

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

Other links and lift over

dbSNP: rs11195417; hg19: chr10-112831994;