rs7111720

Variant names:

• chr11-106242128-T-A
• rs7111720
• ENST00000657948.1:n.545A>T

Variant summary

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

The ENST00000657948.1(ENSG00000286345):​n.545A>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 0.11 in 152,040 control chromosomes in the GnomAD database, including 1,115 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 0.11 (1115 hom., cov: 31)
• Consequence: ENSG00000286345 ENST00000657948.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.426

Genes affected

ENSG00000286345 (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 (AFR) allele frequency at 95% confidence interval = 0.184 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
ENSG00000286345	ENST00000657948.1	n.545A>T		non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16690 AN: 151922 Hom.: 1102 Cov.: 31

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.0560

Gnomad AMR AF: 0.0851

Gnomad ASJ AF: 0.0859

Gnomad EAS AF: 0.00890

Gnomad SAS AF: 0.0962

Gnomad FIN AF: 0.123

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0772

Gnomad OTH AF: 0.104

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.110 AC: 16744 AN: 152040 Hom.: 1115 Cov.: 31 AF XY: 0.112 AC XY: 8307 AN XY: 74308

Gnomad4 AFR AF: 0.188

Gnomad4 AMR AF: 0.0850

Gnomad4 ASJ AF: 0.0859

Gnomad4 EAS AF: 0.00892

Gnomad4 SAS AF: 0.0967

Gnomad4 FIN AF: 0.123

Gnomad4 NFE AF: 0.0772

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0958 Hom.: 78

Bravo AF: 0.111

Asia WGS AF: 0.0680 AC: 238 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	1.3
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7111720; hg19: chr11-106112855;