rs10770141

Variant names:

• chr11-2172610-A-G
• rs10770141
• ENST00000729705.1:n.321-1375A>G

Your query was ambiguous. Multiple possible variants found:

• chr11-2172610-A-G
• chr11-2172610-A-C

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The ENST00000729705.1(ENSG00000295384):​n.321-1375A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000295384 ENST00000729705.1 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: -2.27
• Publications: 61 publications found

Genes affected

ENSG00000295384 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000729705.1. 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
	ENSG00000295384	ENST00000729705.1		n.321-1375A>G		intron	N/A
	ENSG00000295384	ENST00000729706.1		n.372-180A>G		intron	N/A
	ENSG00000295395	ENST00000729780.1		n.397-185T>C		intron	N/A

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

African (AFR) AF: 0.398 AC: 16421 AN: 41304

American (AMR) AF: 0.648 AC: 9905 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2146 AN: 3472

East Asian (EAS) AF: 0.922 AC: 4736 AN: 5134

South Asian (SAS) AF: 0.815 AC: 3925 AN: 4816

European-Finnish (FIN) AF: 0.669 AC: 7062 AN: 10560

Middle Eastern (MID) AF: 0.738 AC: 217 AN: 294

European-Non Finnish (NFE) AF: 0.614 AC: 41726 AN: 67908

Other (OTH) AF: 0.623 AC: 1313 AN: 2106

Alfa AF: 0.615 Hom.: 50670

Bravo AF: 0.568

Asia WGS AF: 0.829 AC: 2883 AN: 3478

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, multiple submitters, no conflicts

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

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.47
DANN	Benign	0.45
PhyloP100		-2.3

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10770141;

hg19: chr11-2193840;