rs884826

Positions:

• chr11-68038662-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000701565.1(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: ENST00000701565.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0250

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000701565.1	n.281C>T		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR AF: 0.295

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.583

Gnomad4 EAS AF: 0.579

Gnomad4 SAS AF: 0.655

Gnomad4 FIN AF: 0.501

Gnomad4 NFE AF: 0.516

Gnomad4 OTH AF: 0.519

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs884826; hg19: chr11-67806129;