10-111076814-A-G

Position:

• chr10-111076814-A-G

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BS1 BS2

The variant allele was found at a frequency of 0.0167 in 151,744 control chromosomes in the GnomAD database, including 45 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency: Genomes: 𝑓 0.017 (45 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.108

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BP6: Variant 10-111076814-A-G is Benign according to our data. Variant chr10-111076814-A-G is described in ClinVar as [Likely_benign]. Clinvar id is 1316601.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0167 (2533/151744) while in subpopulation NFE AF= 0.0237 (1608/67846). AF 95% confidence interval is 0.0227. There are 45 homozygotes in gnomad4. There are 1184 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 45 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0167 AC: 2535 AN: 151628 Hom.: 45 Cov.: 33

Gnomad AFR AF: 0.00436

Gnomad AMI AF: 0.00220

Gnomad AMR AF: 0.0140

Gnomad ASJ AF: 0.0646

Gnomad EAS AF: 0.000195

Gnomad SAS AF: 0.00291

Gnomad FIN AF: 0.0237

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0237

Gnomad OTH AF: 0.0164

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

GnomAD4 genome AF: 0.0167 AC: 2533 AN: 151744 Hom.: 45 Cov.: 33 AF XY: 0.0160 AC XY: 1184 AN XY: 74138

Gnomad4 AFR AF: 0.00435

Gnomad4 AMR AF: 0.0139

Gnomad4 ASJ AF: 0.0646

Gnomad4 EAS AF: 0.000196

Gnomad4 SAS AF: 0.00250

Gnomad4 FIN AF: 0.0237

Gnomad4 NFE AF: 0.0237

Gnomad4 OTH AF: 0.0162

Alfa AF: 0.0192 Hom.: 3

Bravo AF: 0.0159

Asia WGS AF: 0.00260 AC: 10 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

May 13, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	11
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs36022820; hg19: chr10-112836572;