10-111076745-G-C

Position:

• chr10-111076745-G-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.589 in 152,118 control chromosomes in the GnomAD database, including 29,307 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.59 (29307 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.228

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BP6: Variant 10-111076745-G-C is Benign according to our data. Variant chr10-111076745-G-C is described in ClinVar as [Likely_benign]. Clinvar id is 511078.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.731 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: 0.590 AC: 89617 AN: 151998 Hom.: 29317 Cov.: 33

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.762

Gnomad AMR AF: 0.624

Gnomad ASJ AF: 0.722

Gnomad EAS AF: 0.328

Gnomad SAS AF: 0.460

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.620

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.605

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

GnomAD4 genome AF: 0.589 AC: 89624 AN: 152118 Hom.: 29307 Cov.: 33 AF XY: 0.587 AC XY: 43691 AN XY: 74378

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.722

Gnomad4 EAS AF: 0.329

Gnomad4 SAS AF: 0.461

Gnomad4 FIN AF: 0.775

Gnomad4 NFE AF: 0.737

Gnomad4 OTH AF: 0.598

Alfa AF: 0.668 Hom.: 4496

Bravo AF: 0.569

Asia WGS AF: 0.369 AC: 1285 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Mar 09, 2018

This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.5
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1800544; hg19: chr10-112836503; COSMIC: COSV54528958;