10-128622414-G-A

Variant names:

• chr10-128622414-G-A
• rs12359499

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 0.196 in 151,990 control chromosomes in the GnomAD database, including 3,076 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 0.20 (3076 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.323 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: 0.196 AC: 29787 AN: 151874 Hom.: 3075 Cov.: 31

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.208

Gnomad EAS AF: 0.337

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.190

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.196 AC: 29808 AN: 151990 Hom.: 3076 Cov.: 31 AF XY: 0.192 AC XY: 14272 AN XY: 74266

African (AFR) AF: 0.216 AC: 8970 AN: 41478

American (AMR) AF: 0.154 AC: 2354 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.208 AC: 722 AN: 3470

East Asian (EAS) AF: 0.336 AC: 1713 AN: 5100

South Asian (SAS) AF: 0.210 AC: 1009 AN: 4808

European-Finnish (FIN) AF: 0.145 AC: 1534 AN: 10582

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.190 AC: 12903 AN: 67950

Other (OTH) AF: 0.179 AC: 379 AN: 2116

Alfa AF: 0.189 Hom.: 3855

Bravo AF: 0.199

Asia WGS AF: 0.251 AC: 875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.028
DANN	Benign	0.55
PhyloP100		-1.4

Splicing

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

Other links and lift over

dbSNP: rs12359499; hg19: chr10-130420678;