rs659366

chr11-73983709-C-T

Variant summary

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

The ENST00000660751.1(ENSG00000287425):n.261C>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 0.4 in 152,158 control chromosomes in the GnomAD database, including 12,224 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).

• Frequency: Genomes: 𝑓 0.40 (12224 hom., cov: 33)
• Consequence: ENST00000660751.1 non_coding_transcript_exon
• Clinical Significance: risk factor no assertion criteria provided O:1
• Conservation: PhyloP100: -0.0280

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.72).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.448 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
	ENST00000660751.1	n.261C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.401 AC: 60896 AN: 152040 Hom.: 12223 Cov.: 33

Gnomad AFR AF: 0.454

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.427

Gnomad ASJ AF: 0.308

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.398

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.400 AC: 60914 AN: 152158 Hom.: 12224 Cov.: 33 AF XY: 0.401 AC XY: 29808 AN XY: 74366

Gnomad4 AFR AF: 0.453

Gnomad4 AMR AF: 0.428

Gnomad4 ASJ AF: 0.308

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.346

Gnomad4 FIN AF: 0.398

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.372

Alfa AF: 0.371 Hom.: 22135

Bravo AF: 0.406

Asia WGS AF: 0.387 AC: 1343 AN: 3478

ClinVar

Significance: risk factor

Submissions summary: Other:1

Revision: no assertion criteria provided

Submissions by phenotype

Body mass index quantitative trait locus 4 Other:1

risk factor, no assertion criteria provided

literature only

OMIM

Feb 01, 2005

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
Cadd	Benign	4.3
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs659366; hg19: chr11-73694754;