10-111076745-G-C

Variant names:

• chr10-111076745-G-C
• rs1800544

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 169 publications found

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.319 AC: 13256 AN: 41494

American (AMR) AF: 0.623 AC: 9525 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.722 AC: 2501 AN: 3466

East Asian (EAS) AF: 0.329 AC: 1696 AN: 5158

South Asian (SAS) AF: 0.461 AC: 2221 AN: 4820

European-Finnish (FIN) AF: 0.775 AC: 8222 AN: 10608

Middle Eastern (MID) AF: 0.622 AC: 183 AN: 294

European-Non Finnish (NFE) AF: 0.737 AC: 50065 AN: 67972

Other (OTH) AF: 0.598 AC: 1260 AN: 2108

Alfa AF: 0.668 Hom.: 4496

Bravo AF: 0.569

Asia WGS AF: 0.369 AC: 1285 AN: 3478

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.5
DANN	Benign	0.78
PhyloP100		-0.23
PromoterAI		-0.0044	Neutral

Splicing

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

Other links and lift over

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