rs10770140

Variant names:

• chr11-2172367-C-T
• rs10770140
• ENST00000729780.1:n.455G>A

Your query was ambiguous. Multiple possible variants found:

• chr11-2172367-C-T
• chr11-2172367-C-A
• chr11-2172367-C-G

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The ENST00000729780.1(ENSG00000295395):​n.455G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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: ENSG00000295395 ENST00000729780.1 non_coding_transcript_exon
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.829
• Publications: 25 publications found

Genes affected

ENSG00000295395 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729780.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295395	ENST00000729780.1		n.455G>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000295395	ENST00000729781.1		n.479G>A		non_coding_transcript_exon	Exon 3 of 3
	ENSG00000295395	ENST00000729782.1		n.560G>A		non_coding_transcript_exon	Exon 4 of 4

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

African (AFR) AF: 0.474 AC: 19654 AN: 41430

American (AMR) AF: 0.650 AC: 9940 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.646 AC: 2238 AN: 3466

East Asian (EAS) AF: 0.911 AC: 4684 AN: 5140

South Asian (SAS) AF: 0.814 AC: 3928 AN: 4828

European-Finnish (FIN) AF: 0.665 AC: 7039 AN: 10592

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.610 AC: 41398 AN: 67900

Other (OTH) AF: 0.651 AC: 1374 AN: 2110

Alfa AF: 0.609 Hom.: 5674

Bravo AF: 0.591

Asia WGS AF: 0.834 AC: 2901 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	Autosomal recessive DOPA responsive dystonia (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.30
DANN	Benign	0.44
PhyloP100		-0.83

Splicing

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

Other links and lift over

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