10-126858738-A-G

Variant names:

• chr10-126858738-A-G
• rs11245197

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.270 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

Gnomad4 AFR AF: 0.365

Gnomad4 AMR AF: 0.259

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.334

Gnomad4 SAS AF: 0.200

Gnomad4 FIN AF: 0.235

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.274

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11245197; hg19: chr10-128547307;