11-34742932-A-G

Variant names:

• chr11-34742932-A-G
• rs1355223
• ENST00000604513.1:n.27A>G

Variant summary

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

The ENST00000604513.1(ENSG00000270491):​n.27A>G 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 0.476 in 869,892 control chromosomes in the GnomAD database, including 106,270 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 0.42 (15129 hom., cov: 31)
  • Exomes 𝑓: 0.49 (91141 hom.)
• Consequence: ENSG00000270491 ENST00000604513.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.93
• Publications: 10 publications found

Genes affected

ENSG00000270491 (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 (NFE) allele frequency at 95% confidence interval = 0.546 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000604513.1. 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
	ENSG00000270491	ENST00000604513.1	TSL:6	n.27A>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000309692	ENST00000843048.1		n.507-11526A>G		intron	N/A
	ENSG00000309692	ENST00000843049.1		n.699-11526A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.417 AC: 63352 AN: 151928 Hom.: 15123 Cov.: 31

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.759

Gnomad AMR AF: 0.359

Gnomad ASJ AF: 0.538

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.428

Gnomad FIN AF: 0.474

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.461

GnomAD4 exome AF: 0.488 AC: 350651 AN: 717846 Hom.: 91141 Cov.: 9 AF XY: 0.494 AC XY: 190033 AN XY: 385044

African (AFR) AF: 0.214 AC: 4057 AN: 18942

American (AMR) AF: 0.260 AC: 11152 AN: 42884

Ashkenazi Jewish (ASJ) AF: 0.560 AC: 11779 AN: 21024

East Asian (EAS) AF: 0.151 AC: 5392 AN: 35634

South Asian (SAS) AF: 0.451 AC: 32299 AN: 71642

European-Finnish (FIN) AF: 0.485 AC: 24983 AN: 51506

Middle Eastern (MID) AF: 0.556 AC: 2347 AN: 4224

European-Non Finnish (NFE) AF: 0.553 AC: 241615 AN: 436804

Other (OTH) AF: 0.484 AC: 17027 AN: 35186

GnomAD4 genome AF: 0.417 AC: 63369 AN: 152046 Hom.: 15129 Cov.: 31 AF XY: 0.412 AC XY: 30620 AN XY: 74296

African (AFR) AF: 0.218 AC: 9065 AN: 41508

American (AMR) AF: 0.358 AC: 5468 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.538 AC: 1868 AN: 3470

East Asian (EAS) AF: 0.130 AC: 670 AN: 5172

South Asian (SAS) AF: 0.429 AC: 2067 AN: 4820

European-Finnish (FIN) AF: 0.474 AC: 4990 AN: 10528

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.551 AC: 37453 AN: 67960

Other (OTH) AF: 0.456 AC: 963 AN: 2112

Alfa AF: 0.506 Hom.: 25637

Bravo AF: 0.395

Asia WGS AF: 0.226 AC: 786 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	3.7
DANN	Benign	0.51
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs1355223; hg19: chr11-34764479;