rs1355223

Positions:

• chr11-34742932-A-G

Variant summary

Our verdict is Benign. Variant got -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: ENST00000604513.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.93

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC102723568	XR_007062652.1	n.894+10503A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000604513.1	n.27A>G		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR exome AF: 0.214

Gnomad4 AMR exome AF: 0.260

Gnomad4 ASJ exome AF: 0.560

Gnomad4 EAS exome AF: 0.151

Gnomad4 SAS exome AF: 0.451

Gnomad4 FIN exome AF: 0.485

Gnomad4 NFE exome AF: 0.553

Gnomad4 OTH exome AF: 0.484

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

Gnomad4 AFR AF: 0.218

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.538

Gnomad4 EAS AF: 0.130

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.474

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.456

Alfa AF: 0.523 Hom.: 20511

Bravo AF: 0.395

Asia WGS AF: 0.226 AC: 786 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	3.7
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1355223; hg19: chr11-34764479;