11-2172367-C-T

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 0.599 in 151,962 control chromosomes in the GnomAD database, including 27,941 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.60 (27941 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.829

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP6: Variant 11-2172367-C-T is Benign according to our data. Variant chr11-2172367-C-T is described in ClinVar as [Benign]. Clinvar id is 1168271.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

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: 0.599 AC: 91006 AN: 151844 Hom.: 27934 Cov.: 33

Gnomad AFR AF: 0.475

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.646

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.814

Gnomad FIN AF: 0.665

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.648

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

GnomAD4 genome AF: 0.599 AC: 91036 AN: 151962 Hom.: 27941 Cov.: 33 AF XY: 0.609 AC XY: 45220 AN XY: 74286

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.650

Gnomad4 ASJ AF: 0.646

Gnomad4 EAS AF: 0.911

Gnomad4 SAS AF: 0.814

Gnomad4 FIN AF: 0.665

Gnomad4 NFE AF: 0.610

Gnomad4 OTH AF: 0.651

Alfa AF: 0.609 Hom.: 5674

Bravo AF: 0.591

Asia WGS AF: 0.834 AC: 2901 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Autosomal recessive DOPA responsive dystonia Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 22, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.30
Dann	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10770140; hg19: chr11-2193597; COSMIC: COSV60768294;