rs11730243

chr4-105542556-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001741413.2(LOC105377352):n.561G>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: LOC105377352 XR_001741413.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.415

Genes affected

LOC105377352 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105377352	XR_001741413.2	n.561G>A		non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000514879.1	n.302+15G>A		intron_variant, non_coding_transcript_variant		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

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

Gnomad4 AFR AF: 0.324

Gnomad4 AMR AF: 0.517

Gnomad4 ASJ AF: 0.630

Gnomad4 EAS AF: 0.412

Gnomad4 SAS AF: 0.607

Gnomad4 FIN AF: 0.674

Gnomad4 NFE AF: 0.728

Gnomad4 OTH AF: 0.592

Alfa AF: 0.694 Hom.: 61238

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11730243; hg19: chr4-106463713;