rs11628587

Variant names:

• chr14-60240713-C-T
• rs11628587
• ENST00000532515.1:n.2267G>A

Variant summary

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

The ENST00000532515.1(ENSG00000254718):​n.2267G>A 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 0.346 in 152,054 control chromosomes in the GnomAD database, including 9,878 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 0.35 (9878 hom., cov: 33)
  • Exomes 𝑓: 0.30 (0 hom.)
• Consequence: ENSG00000254718 ENST00000532515.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.440
• Publications: 3 publications found

Genes affected

ENSG00000254718 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000532515.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101927702	NR_188027.1		n.201-259G>A		intron	N/A
	LOC101927702	NR_188028.1		n.280-259G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254718	ENST00000532515.1	TSL:1	n.2267G>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000254718	ENST00000529171.5	TSL:3	n.235-259G>A		intron	N/A
	ENSG00000254718	ENST00000553269.6	TSL:3	n.283-259G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.345 AC: 52486 AN: 151924 Hom.: 9861 Cov.: 33

Gnomad AFR AF: 0.500

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.267

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.128

Gnomad SAS AF: 0.441

Gnomad FIN AF: 0.261

Gnomad MID AF: 0.383

Gnomad NFE AF: 0.293

Gnomad OTH AF: 0.325

GnomAD4 exome AF: 0.300 AC: 3 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.300 AC XY: 3 AN XY: 10

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 0.500 AC: 1 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.250 AC: 2 AN: 8

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.346 AC: 52544 AN: 152044 Hom.: 9878 Cov.: 33 AF XY: 0.341 AC XY: 25326 AN XY: 74306

African (AFR) AF: 0.500 AC: 20751 AN: 41464

American (AMR) AF: 0.266 AC: 4070 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1400 AN: 3470

East Asian (EAS) AF: 0.129 AC: 666 AN: 5170

South Asian (SAS) AF: 0.439 AC: 2116 AN: 4824

European-Finnish (FIN) AF: 0.261 AC: 2756 AN: 10568

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.293 AC: 19912 AN: 67946

Other (OTH) AF: 0.321 AC: 679 AN: 2112

Alfa AF: 0.315 Hom.: 1470

Bravo AF: 0.350

Asia WGS AF: 0.275 AC: 959 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	7.9
DANN	Benign	0.80
PhyloP100		0.44

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs11628587;

hg19: chr14-60707431;