ENST00000531511.1:n.409G>A

Variant names:

• chr11-76654411-C-T
• rs11236836
• ENST00000531511.1:n.409G>A

Variant summary

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

The ENST00000531511.1(ENSG00000254810):​n.409G>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 0.502 in 152,018 control chromosomes in the GnomAD database, including 19,444 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 0.50 (19430 hom., cov: 32)
  • Exomes 𝑓: 0.52 (14 hom.)
• Consequence: ENSG00000254810 ENST00000531511.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.551
• Publications: 1 publications found

Genes affected

ENSG00000254810 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000531511.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254810	ENST00000531511.1	TSL:3	n.409G>A		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000254810	ENST00000686694.2		n.493-554G>A		intron	N/A
	ENSG00000254810	ENST00000739657.1		n.454+2038G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.502 AC: 76207 AN: 151810 Hom.: 19412 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.569

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.544

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.511

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.531

Gnomad OTH AF: 0.479

GnomAD4 exome AF: 0.522 AC: 47 AN: 90 Hom.: 14 Cov.: 0 AF XY: 0.517 AC XY: 30 AN XY: 58

African (AFR) AF: 0.667 AC: 4 AN: 6

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 0.750 AC: 3 AN: 4

South Asian (SAS) AF: 0.750 AC: 3 AN: 4

European-Finnish (FIN) AF: 0.583 AC: 7 AN: 12

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.442 AC: 23 AN: 52

Other (OTH) AF: 0.583 AC: 7 AN: 12

GnomAD4 genome AF: 0.502 AC: 76262 AN: 151928 Hom.: 19430 Cov.: 32 AF XY: 0.499 AC XY: 37035 AN XY: 74228

African (AFR) AF: 0.466 AC: 19320 AN: 41420

American (AMR) AF: 0.449 AC: 6859 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1582 AN: 3472

East Asian (EAS) AF: 0.544 AC: 2806 AN: 5158

South Asian (SAS) AF: 0.535 AC: 2573 AN: 4812

European-Finnish (FIN) AF: 0.511 AC: 5383 AN: 10536

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.531 AC: 36085 AN: 67930

Other (OTH) AF: 0.480 AC: 1011 AN: 2106

Alfa AF: 0.510 Hom.: 23710

Bravo AF: 0.497

Asia WGS AF: 0.550 AC: 1915 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.46
DANN	Benign	0.67
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs11236836; hg19: chr11-76365455;