rs659366

Variant names:

• chr11-73983709-C-T
• rs659366
• ENST00000660751.1:n.261C>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: ENSG00000287425 ENST00000660751.1 non_coding_transcript_exon
• Clinical Significance: risk factor no assertion criteria provided O:1
• Conservation: PhyloP100: -0.0280

Genes affected

ENSG00000287425 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287425	ENST00000660751.1	n.261C>T		non_coding_transcript_exon_variant	Exon 1 of 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

Feb 01, 2005

OMIM

Significance: risk factor

Review Status: no assertion criteria provided

Collection Method: literature only

- -

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;