chr11-68038662-G-A

Variant names:

• chr11-68038662-G-A
• rs884826
• ENST00000701565.2:n.281C>T

Variant summary

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

The ENST00000701565.2(ENSG00000289908):​n.281C>T 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 0.47 in 152,038 control chromosomes in the GnomAD database, including 17,743 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 0.47 (17743 hom., cov: 33)
• Consequence: ENSG00000289908 ENST00000701565.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250
• Publications: 7 publications found

Genes affected

ENSG00000289908 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.636 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
ENSG00000289908	ENST00000701565.2	n.281C>T		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.470 AC: 71382 AN: 151920 Hom.: 17739 Cov.: 33

Gnomad AFR AF: 0.296

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.579

Gnomad SAS AF: 0.656

Gnomad FIN AF: 0.501

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.516

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.470 AC: 71401 AN: 152038 Hom.: 17743 Cov.: 33 AF XY: 0.474 AC XY: 35228 AN XY: 74308

African (AFR) AF: 0.295 AC: 12261 AN: 41514

American (AMR) AF: 0.592 AC: 9052 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.583 AC: 2024 AN: 3472

East Asian (EAS) AF: 0.579 AC: 2977 AN: 5142

South Asian (SAS) AF: 0.655 AC: 3152 AN: 4810

European-Finnish (FIN) AF: 0.501 AC: 5301 AN: 10588

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.516 AC: 35068 AN: 67912

Other (OTH) AF: 0.519 AC: 1094 AN: 2108

Alfa AF: 0.491 Hom.: 2365

Bravo AF: 0.472

Asia WGS AF: 0.582 AC: 2020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.9
DANN	Benign	0.87
PhyloP100		-0.025
PromoterAI		-0.025	Neutral

Splicing

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

Other links and lift over

dbSNP: rs884826; hg19: chr11-67806129;