11-2174751-T-C

Variant names:

• chr11-2174751-T-C
• rs10743152
• ENST00000729780.1:n.346A>G

Variant summary

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

The ENST00000729780.1(ENSG00000295395):​n.346A>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 0.641 in 152,122 control chromosomes in the GnomAD database, including 31,530 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 0.64 (31530 hom., cov: 34)
• Consequence: ENSG00000295395 ENST00000729780.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 19 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.894 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
ENSG00000295395	ENST00000729780.1	n.346A>G		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000295395	ENST00000729781.1	n.370A>G		non_coding_transcript_exon_variant	Exon 2 of 3
ENSG00000295395	ENST00000729782.1	n.451A>G		non_coding_transcript_exon_variant	Exon 3 of 4
ENSG00000295395	ENST00000729783.1	n.299A>G		non_coding_transcript_exon_variant	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97450 AN: 152004 Hom.: 31526 Cov.: 34

Gnomad AFR AF: 0.593

Gnomad AMI AF: 0.607

Gnomad AMR AF: 0.687

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.915

Gnomad SAS AF: 0.816

Gnomad FIN AF: 0.667

Gnomad MID AF: 0.787

Gnomad NFE AF: 0.622

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.641 AC: 97478 AN: 152122 Hom.: 31530 Cov.: 34 AF XY: 0.649 AC XY: 48243 AN XY: 74388

African (AFR) AF: 0.592 AC: 24572 AN: 41498

American (AMR) AF: 0.686 AC: 10497 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.636 AC: 2207 AN: 3472

East Asian (EAS) AF: 0.916 AC: 4719 AN: 5154

South Asian (SAS) AF: 0.815 AC: 3935 AN: 4828

European-Finnish (FIN) AF: 0.667 AC: 7076 AN: 10602

Middle Eastern (MID) AF: 0.805 AC: 235 AN: 292

European-Non Finnish (NFE) AF: 0.622 AC: 42236 AN: 67956

Other (OTH) AF: 0.685 AC: 1449 AN: 2114

Alfa AF: 0.637 Hom.: 63937

Bravo AF: 0.639

Asia WGS AF: 0.846 AC: 2939 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	6.5
DANN	Benign	0.39
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs10743152; hg19: chr11-2195981; COSMIC: COSV60768768;