chr10-91728797-T-A

Position:

• chr10-91728797-T-A

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 0.38 in 152,056 control chromosomes in the GnomAD database, including 11,497 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 0.38 (11497 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.688

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.380 AC: 57757 AN: 151938 Hom.: 11488 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.464

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.572

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.366

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.350

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

GnomAD4 genome AF: 0.380 AC: 57790 AN: 152056 Hom.: 11497 Cov.: 32 AF XY: 0.392 AC XY: 29169 AN XY: 74326

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.423

Gnomad4 ASJ AF: 0.464

Gnomad4 EAS AF: 0.628

Gnomad4 SAS AF: 0.570

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.347

Alfa AF: 0.361 Hom.: 1227

Bravo AF: 0.365

Asia WGS AF: 0.559 AC: 1940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.9
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7100340; hg19: chr10-93488554;