rs7114854

Variant names:

• chr11-5122692-C-A
• rs7114854
• ENST00000498233.5:n.202G>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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: ENSG00000290651 ENST00000498233.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0390
• Publications: 2 publications found

Genes affected

ENSG00000290651 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290651	ENST00000498233.5	n.202G>T		non_coding_transcript_exon_variant	Exon 3 of 4	6
ENSG00000290651	ENST00000481634.1	n.47-785G>T		intron_variant	Intron 1 of 1	6

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

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

African (AFR) AF: 0.773 AC: 31879 AN: 41234

American (AMR) AF: 0.693 AC: 10478 AN: 15114

Ashkenazi Jewish (ASJ) AF: 0.716 AC: 2482 AN: 3468

East Asian (EAS) AF: 0.561 AC: 2862 AN: 5104

South Asian (SAS) AF: 0.714 AC: 3421 AN: 4794

European-Finnish (FIN) AF: 0.714 AC: 7345 AN: 10294

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.707 AC: 47933 AN: 67770

Other (OTH) AF: 0.742 AC: 1555 AN: 2096

Alfa AF: 0.684 Hom.: 2857

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
PhyloP100		-0.039

Splicing

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

Other links and lift over

dbSNP: rs7114854; hg19: chr11-5143922;