rs7106715

Variant names:

• chr11-133969010-C-T
• rs7106715
• ENST00000763462.1:n.258+1288C>T

Variant summary

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

The ENST00000763462.1(ENSG00000299430):​n.258+1288C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.158 in 152,254 control chromosomes in the GnomAD database, including 2,495 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 0.16 (2495 hom., cov: 33)
• Consequence: ENSG00000299430 ENST00000763462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.331
• Publications: 2 publications found

Genes affected

ENSG00000299430 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.216 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000763462.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299430	ENST00000763462.1		n.258+1288C>T		intron	N/A
	ENSG00000299430	ENST00000763463.1		n.368+1136C>T		intron	N/A
	ENSG00000299430	ENST00000763464.1		n.222+1271C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.158 AC: 24061 AN: 152136 Hom.: 2496 Cov.: 33

Gnomad AFR AF: 0.0473

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.138

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.0438

Gnomad SAS AF: 0.121

Gnomad FIN AF: 0.294

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.219

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.158 AC: 24061 AN: 152254 Hom.: 2495 Cov.: 33 AF XY: 0.159 AC XY: 11833 AN XY: 74434

African (AFR) AF: 0.0473 AC: 1966 AN: 41554

American (AMR) AF: 0.138 AC: 2115 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 518 AN: 3470

East Asian (EAS) AF: 0.0438 AC: 227 AN: 5188

South Asian (SAS) AF: 0.120 AC: 582 AN: 4830

European-Finnish (FIN) AF: 0.294 AC: 3120 AN: 10596

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.219 AC: 14889 AN: 68006

Other (OTH) AF: 0.136 AC: 287 AN: 2114

Alfa AF: 0.182 Hom.: 548

Bravo AF: 0.139

Asia WGS AF: 0.0630 AC: 219 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.57
PhyloP100		-0.33

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7106715;

hg19: chr11-133838905;