10-80289847-A-G

Position:

• chr10-80289847-A-G

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 0.102 in 152,238 control chromosomes in the GnomAD database, including 1,025 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.10 (1025 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.109

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 10-80289847-A-G is Benign according to our data. Variant chr10-80289847-A-G is described in ClinVar as [Benign]. Clinvar id is 1262908.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.253 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: 0.102 AC: 15475 AN: 152120 Hom.: 1012 Cov.: 32

Gnomad AFR AF: 0.0425

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.104

Gnomad EAS AF: 0.0208

Gnomad SAS AF: 0.264

Gnomad FIN AF: 0.0719

Gnomad MID AF: 0.101

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.111

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

GnomAD4 genome AF: 0.102 AC: 15512 AN: 152238 Hom.: 1025 Cov.: 32 AF XY: 0.103 AC XY: 7703 AN XY: 74448

Gnomad4 AFR AF: 0.0427

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.104

Gnomad4 EAS AF: 0.0208

Gnomad4 SAS AF: 0.265

Gnomad4 FIN AF: 0.0719

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.115

Alfa AF: 0.101 Hom.: 136

Bravo AF: 0.105

Asia WGS AF: 0.164 AC: 572 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 22, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	7.6
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17677908; hg19: chr10-82049603;