chr10-122354840-A-G

Variant names:

• chr10-122354840-A-G
• rs7904674

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 0.188 in 152,186 control chromosomes in the GnomAD database, including 3,080 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 0.19 (3080 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.166
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.239 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: 0.188 AC: 28539 AN: 152068 Hom.: 3077 Cov.: 33

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.309

Gnomad EAS AF: 0.0565

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.256

Gnomad NFE AF: 0.243

Gnomad OTH AF: 0.226

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

GnomAD4 genome AF: 0.188 AC: 28540 AN: 152186 Hom.: 3080 Cov.: 33 AF XY: 0.184 AC XY: 13653 AN XY: 74400

African (AFR) AF: 0.114 AC: 4754 AN: 41534

American (AMR) AF: 0.167 AC: 2550 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.309 AC: 1072 AN: 3472

East Asian (EAS) AF: 0.0568 AC: 295 AN: 5190

South Asian (SAS) AF: 0.193 AC: 930 AN: 4826

European-Finnish (FIN) AF: 0.163 AC: 1728 AN: 10570

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.243 AC: 16487 AN: 67984

Other (OTH) AF: 0.224 AC: 474 AN: 2116

Alfa AF: 0.226 Hom.: 18110

Bravo AF: 0.184

Asia WGS AF: 0.101 AC: 352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.46
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs7904674; hg19: chr10-124114356;