chr11-35063906-T-G

Variant names:

• chr11-35063906-T-G
• rs2553772
• ENST00000748195.1:n.785A>C

Variant summary

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

The ENST00000748195.1(ENSG00000289526):​n.785A>C 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 0.51 in 151,902 control chromosomes in the GnomAD database, including 20,702 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 0.51 (20702 hom., cov: 31)
• Consequence: ENSG00000289526 ENST00000748195.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.618
• Publications: 8 publications found

Genes affected

ENSG00000289526 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376626	XR_001748180.2	n.705+1214A>C		intron_variant	Intron 2 of 3
LOC105376626	XR_007062653.1	n.705+1214A>C		intron_variant	Intron 2 of 4
LOC105376626	XR_007062654.1	n.705+1214A>C		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289526	ENST00000748195.1	n.785A>C		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000289526	ENST00000685560.2	n.443+1214A>C		intron_variant	Intron 2 of 2
ENSG00000289526	ENST00000701115.2	n.662+1214A>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77401 AN: 151784 Hom.: 20697 Cov.: 31

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.510 AC: 77418 AN: 151902 Hom.: 20702 Cov.: 31 AF XY: 0.515 AC XY: 38242 AN XY: 74262

African (AFR) AF: 0.349 AC: 14470 AN: 41422

American (AMR) AF: 0.601 AC: 9180 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2114 AN: 3468

East Asian (EAS) AF: 0.753 AC: 3880 AN: 5150

South Asian (SAS) AF: 0.689 AC: 3311 AN: 4808

European-Finnish (FIN) AF: 0.514 AC: 5425 AN: 10562

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37197 AN: 67910

Other (OTH) AF: 0.545 AC: 1149 AN: 2108

Alfa AF: 0.378 Hom.: 1027

Bravo AF: 0.507

Asia WGS AF: 0.685 AC: 2384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.0
DANN	Benign	0.71
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs2553772; hg19: chr11-35085453;