11-2172610-A-G

Variant names:

• chr11-2172610-A-G
• rs10770141

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The variant allele was found at a frequency of 0.58 in 151,788 control chromosomes in the GnomAD database, including 26,680 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency: Genomes: 𝑓 0.58 (26680 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -2.27

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BP6: Variant 11-2172610-A-G is Benign according to our data. Variant chr11-2172610-A-G is described in ClinVar as [Benign]. Clinvar id is 1164244.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.901 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: 0.580 AC: 87979 AN: 151670 Hom.: 26673 Cov.: 31

Gnomad AFR AF: 0.398

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.648

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.815

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.620

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

GnomAD4 genome AF: 0.580 AC: 88003 AN: 151788 Hom.: 26680 Cov.: 31 AF XY: 0.590 AC XY: 43761 AN XY: 74174

Gnomad4 AFR AF: 0.398

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.922

Gnomad4 SAS AF: 0.815

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.614

Gnomad4 OTH AF: 0.623

Alfa AF: 0.624 Hom.: 38615

Bravo AF: 0.568

Asia WGS AF: 0.829 AC: 2883 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Schizophrenia Benign:1

-

Center for Forensic Mental Health, Chiba University

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: case-control

- -

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

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.47
DANN	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10770141; hg19: chr11-2193840;