10-111076745-G-C

Variant names:

• chr10-111076745-G-C
• rs1800544

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

Mar 09, 2018

GeneDx

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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;