10-83110320-T-C

Variant names:

• chr10-83110320-T-C
• rs7915137

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 0.372 in 151,918 control chromosomes in the GnomAD database, including 10,724 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 0.37 (10724 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.658

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.456 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: 0.373 AC: 56551 AN: 151802 Hom.: 10715 Cov.: 32

Gnomad AFR AF: 0.407

Gnomad AMI AF: 0.463

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.450

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.299

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.347

Gnomad OTH AF: 0.377

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

GnomAD4 genome AF: 0.372 AC: 56583 AN: 151918 Hom.: 10724 Cov.: 32 AF XY: 0.372 AC XY: 27630 AN XY: 74272

Gnomad4 AFR AF: 0.407

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.450

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.299

Gnomad4 NFE AF: 0.347

Gnomad4 OTH AF: 0.376

Alfa AF: 0.356 Hom.: 20091

Bravo AF: 0.380

Asia WGS AF: 0.419 AC: 1457 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7915137; hg19: chr10-84870076;