chr7-13861106-A-G

Variant names:

• chr7-13861106-A-G
• rs7795991
• ENST00000654062.1:n.483+530T>C

Variant summary

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

The ENST00000654062.1(ENSG00000224330):​n.483+530T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 152,044 control chromosomes in the GnomAD database, including 20,352 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 0.52 (20352 hom., cov: 33)
• Consequence: ENSG00000224330 ENST00000654062.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.829
• Publications: 13 publications found

Genes affected

ENSG00000224330 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.538 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654062.1. 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
	ENSG00000224330	ENST00000654062.1		n.483+530T>C		intron	N/A
	ENSG00000224330	ENST00000835227.1		n.95-2083T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.516 AC: 78350 AN: 151924 Hom.: 20325 Cov.: 33

Gnomad AFR AF: 0.544

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.503

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.401

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.504

Gnomad OTH AF: 0.515

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

GnomAD4 genome AF: 0.516 AC: 78428 AN: 152044 Hom.: 20352 Cov.: 33 AF XY: 0.516 AC XY: 38354 AN XY: 74328

African (AFR) AF: 0.544 AC: 22547 AN: 41464

American (AMR) AF: 0.504 AC: 7698 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1681 AN: 3472

East Asian (EAS) AF: 0.400 AC: 2068 AN: 5164

South Asian (SAS) AF: 0.542 AC: 2616 AN: 4824

European-Finnish (FIN) AF: 0.549 AC: 5803 AN: 10566

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.504 AC: 34226 AN: 67968

Other (OTH) AF: 0.518 AC: 1092 AN: 2110

Alfa AF: 0.506 Hom.: 80802

Bravo AF: 0.512

Asia WGS AF: 0.532 AC: 1852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.7
DANN	Benign	0.61
PhyloP100		0.83

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: rs7795991;

hg19: chr7-13900731;