11-2172367-C-T

Variant names:

• chr11-2172367-C-T
• rs10770140

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

Jan 15, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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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;