chr10-6658154-A-G

Variant names:

• chr10-6658154-A-G
• rs11253857

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 0.145 in 152,206 control chromosomes in the GnomAD database, including 1,935 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 0.15 (1935 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.25 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: 0.145 AC: 22102 AN: 152088 Hom.: 1935 Cov.: 32

Gnomad AFR AF: 0.0606

Gnomad AMI AF: 0.186

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.261

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.145 AC: 22100 AN: 152206 Hom.: 1935 Cov.: 32 AF XY: 0.147 AC XY: 10936 AN XY: 74404

African (AFR) AF: 0.0606 AC: 2516 AN: 41548

American (AMR) AF: 0.144 AC: 2200 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.152 AC: 528 AN: 3470

East Asian (EAS) AF: 0.215 AC: 1117 AN: 5188

South Asian (SAS) AF: 0.262 AC: 1267 AN: 4830

European-Finnish (FIN) AF: 0.175 AC: 1847 AN: 10578

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.178 AC: 12103 AN: 67980

Other (OTH) AF: 0.150 AC: 317 AN: 2112

Alfa AF: 0.171 Hom.: 4414

Bravo AF: 0.138

Asia WGS AF: 0.230 AC: 799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.35
PhyloP100		0.078

Splicing

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

Other links and lift over

dbSNP: rs11253857; hg19: chr10-6700116;