rs11564710

Variant names:

• chr11-2179099-A-C
• rs11564710
• ENST00000729780.1:n.164T>G

Your query was ambiguous. Multiple possible variants found:

• chr11-2179099-A-C
• chr11-2179099-A-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000729780.1(ENSG00000295395):​n.164T>G 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 0.462 in 152,170 control chromosomes in the GnomAD database, including 19,037 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.46 (19037 hom., cov: 34)
• Consequence: ENSG00000295395 ENST00000729780.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.277
• Publications: 11 publications found

Genes affected

ENSG00000295395 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.758 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295395	ENST00000729780.1		n.164T>G		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000295409	ENST00000729856.1		n.177+1051A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.463 AC: 70377 AN: 152052 Hom.: 19048 Cov.: 34

Gnomad AFR AF: 0.167

Gnomad AMI AF: 0.481

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.668

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.655

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.522

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

GnomAD4 genome AF: 0.462 AC: 70363 AN: 152170 Hom.: 19037 Cov.: 34 AF XY: 0.471 AC XY: 35052 AN XY: 74390

African (AFR) AF: 0.167 AC: 6918 AN: 41526

American (AMR) AF: 0.459 AC: 7018 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1846 AN: 3468

East Asian (EAS) AF: 0.778 AC: 4038 AN: 5188

South Asian (SAS) AF: 0.668 AC: 3223 AN: 4824

European-Finnish (FIN) AF: 0.618 AC: 6555 AN: 10602

Middle Eastern (MID) AF: 0.667 AC: 196 AN: 294

European-Non Finnish (NFE) AF: 0.574 AC: 39032 AN: 67962

Other (OTH) AF: 0.523 AC: 1098 AN: 2100

Alfa AF: 0.530 Hom.: 50407

Bravo AF: 0.439

Asia WGS AF: 0.677 AC: 2356 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.6
DANN	Benign	0.53
PhyloP100		0.28

Splicing

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

Other links and lift over

dbSNP: rs11564710; hg19: chr11-2200329;