chr10-126858738-A-G

Variant names:

• chr10-126858738-A-G
• rs11245197

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 0.27 in 152,026 control chromosomes in the GnomAD database, including 5,960 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 0.27 (5960 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.59
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.36 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.270 AC: 41066 AN: 151908 Hom.: 5950 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.138

Gnomad AMR AF: 0.259

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.201

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.270 AC: 41101 AN: 152026 Hom.: 5960 Cov.: 32 AF XY: 0.270 AC XY: 20094 AN XY: 74308

African (AFR) AF: 0.365 AC: 15138 AN: 41444

American (AMR) AF: 0.259 AC: 3958 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.265 AC: 918 AN: 3470

East Asian (EAS) AF: 0.334 AC: 1719 AN: 5146

South Asian (SAS) AF: 0.200 AC: 965 AN: 4822

European-Finnish (FIN) AF: 0.235 AC: 2490 AN: 10574

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15106 AN: 67972

Other (OTH) AF: 0.274 AC: 579 AN: 2114

Alfa AF: 0.193 Hom.: 613

Bravo AF: 0.284

Asia WGS AF: 0.259 AC: 899 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.043
DANN	Benign	0.26
PhyloP100		-2.6

Splicing

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

Other links and lift over

dbSNP: rs11245197; hg19: chr10-128547307;