chr10-7689020-C-T

Variant names:

• chr10-7689020-C-T
• rs11812109

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 0.157 in 151,624 control chromosomes in the GnomAD database, including 2,097 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 (2097 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.241 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: 0.157 AC: 23712 AN: 151506 Hom.: 2091 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.0784

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.113

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.0882

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.143

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

GnomAD4 genome AF: 0.157 AC: 23749 AN: 151624 Hom.: 2097 Cov.: 32 AF XY: 0.154 AC XY: 11433 AN XY: 74086

African (AFR) AF: 0.245 AC: 10099 AN: 41280

American (AMR) AF: 0.136 AC: 2079 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.113 AC: 392 AN: 3466

East Asian (EAS) AF: 0.132 AC: 679 AN: 5154

South Asian (SAS) AF: 0.0876 AC: 420 AN: 4794

European-Finnish (FIN) AF: 0.126 AC: 1322 AN: 10496

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8357 AN: 67890

Other (OTH) AF: 0.146 AC: 308 AN: 2106

Alfa AF: 0.130 Hom.: 1956

Bravo AF: 0.161

Asia WGS AF: 0.117 AC: 405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.21
DANN	Benign	0.48
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs11812109; hg19: chr10-7730983;