chr10-97688247-C-T

Variant names:

• chr10-97688247-C-T
• rs11189328

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 0.195 in 151,980 control chromosomes in the GnomAD database, including 2,988 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 (2988 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.278 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: 0.194 AC: 29524 AN: 151862 Hom.: 2982 Cov.: 32

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.236

Gnomad AMR AF: 0.190

Gnomad ASJ AF: 0.224

Gnomad EAS AF: 0.205

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.195 AC: 29561 AN: 151980 Hom.: 2988 Cov.: 32 AF XY: 0.192 AC XY: 14300 AN XY: 74312

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.190

Gnomad4 ASJ AF: 0.224

Gnomad4 EAS AF: 0.205

Gnomad4 SAS AF: 0.290

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.204

Alfa AF: 0.198 Hom.: 293

Bravo AF: 0.199

Asia WGS AF: 0.247 AC: 859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.8
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11189328; hg19: chr10-99448004;