rs7114854

Positions:

• chr11-5122692-C-A
• chr11-5122692-C-G
• chr11-5122692-C-T

Variant summary

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

The ENST00000498233.5(ENSG00000290651):​n.202G>T 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 0.72 in 151,074 control chromosomes in the GnomAD database, including 39,184 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 0.72 (39184 hom., cov: 29)
  • Failed GnomAD Quality Control
• Consequence: ENST00000498233.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000498233.5	n.202G>T		non_coding_transcript_exon_variant	3/4
	ENST00000481634.1	n.47-785G>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.719 AC: 108598 AN: 150958 Hom.: 39132 Cov.: 29

Gnomad AFR AF: 0.773

Gnomad AMI AF: 0.600

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.561

Gnomad SAS AF: 0.712

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.740

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: 0.720 AC: 108707 AN: 151074 Hom.: 39184 Cov.: 29 AF XY: 0.718 AC XY: 52929 AN XY: 73710

Gnomad4 AFR AF: 0.773

Gnomad4 AMR AF: 0.693

Gnomad4 ASJ AF: 0.716

Gnomad4 EAS AF: 0.561

Gnomad4 SAS AF: 0.714

Gnomad4 FIN AF: 0.714

Gnomad4 NFE AF: 0.707

Gnomad4 OTH AF: 0.742

Alfa AF: 0.679 Hom.: 2627

Bravo AF: 0.720

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.1
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7114854; hg19: chr11-5143922;