rs11730243

Variant names:

• chr4-105542556-C-T
• rs11730243
• ENST00000833611.1:n.399G>A

Variant summary

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

The ENST00000833611.1(ENSG00000250522):​n.399G>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 0.574 in 151,698 control chromosomes in the GnomAD database, including 27,360 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 0.57 (27360 hom., cov: 31)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000250522 ENST00000833611.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415
• Publications: 9 publications found

Genes affected

ENSG00000250522 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.723 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377352	NR_188419.1	n.246G>A		non_coding_transcript_exon_variant	Exon 2 of 4
LOC105377352	NR_188418.1	n.231+15G>A		intron_variant	Intron 2 of 4
LOC105377352	NR_188420.1	n.93-1080G>A		intron_variant	Intron 1 of 2
LOC105377352	NR_188421.1	n.86-1080G>A		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250522	ENST00000833611.1	n.399G>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000250522	ENST00000514879.1	n.302+15G>A		intron_variant	Intron 2 of 3	4

Frequencies

GnomAD3 genomes AF: 0.575 AC: 87107 AN: 151578 Hom.: 27365 Cov.: 31

Gnomad AFR AF: 0.325

Gnomad AMI AF: 0.776

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.412

Gnomad SAS AF: 0.606

Gnomad FIN AF: 0.674

Gnomad MID AF: 0.557

Gnomad NFE AF: 0.728

Gnomad OTH AF: 0.598

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

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) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.574 AC: 87102 AN: 151698 Hom.: 27360 Cov.: 31 AF XY: 0.567 AC XY: 42011 AN XY: 74128

African (AFR) AF: 0.324 AC: 13412 AN: 41396

American (AMR) AF: 0.517 AC: 7860 AN: 15202

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2182 AN: 3466

East Asian (EAS) AF: 0.412 AC: 2124 AN: 5156

South Asian (SAS) AF: 0.607 AC: 2927 AN: 4822

European-Finnish (FIN) AF: 0.674 AC: 7118 AN: 10560

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.728 AC: 49362 AN: 67788

Other (OTH) AF: 0.592 AC: 1245 AN: 2102

Alfa AF: 0.666 Hom.: 96468

Bravo AF: 0.548

Asia WGS AF: 0.484 AC: 1683 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.58
PhyloP100		-0.41

Splicing

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

Other links and lift over

dbSNP: rs11730243; hg19: chr4-106463713;