rs7648568

Variant names:

• chr3-137341847-C-T
• rs7648568
• ENST00000733950.1:n.-50G>A

Variant summary

Our verdict is Benign. The variant received -9 ACMG points: 0P and 9B. BP4 BA1

The ENST00000733950.1(ENSG00000295924):​n.-50G>A variant causes a upstream gene change. The variant allele was found at a frequency of 0.184 in 152,122 control chromosomes in the GnomAD database, including 2,808 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 0.18 (2808 hom., cov: 33)
• Consequence: ENSG00000295924 ENST00000733950.1 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 5.15
• Publications: 2 publications found

Genes affected

ENSG00000295924 (HGNC:58946):

ACMG classification

Our verdict: Benign. The variant received -9 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.17).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.378 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000733950.1. 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
	ENSG00000295924	ENST00000733950.1		n.-50G>A		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.185 AC: 28053 AN: 152004 Hom.: 2803 Cov.: 33

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.164

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.166

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.184 AC: 28063 AN: 152122 Hom.: 2808 Cov.: 33 AF XY: 0.187 AC XY: 13897 AN XY: 74384

African (AFR) AF: 0.206 AC: 8556 AN: 41512

American (AMR) AF: 0.164 AC: 2507 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 695 AN: 3468

East Asian (EAS) AF: 0.176 AC: 912 AN: 5184

South Asian (SAS) AF: 0.393 AC: 1894 AN: 4818

European-Finnish (FIN) AF: 0.161 AC: 1696 AN: 10566

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.166 AC: 11279 AN: 67972

Other (OTH) AF: 0.183 AC: 386 AN: 2108

Alfa AF: 0.0994 Hom.: 147

Bravo AF: 0.183

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.17
CADD	Uncertain	24
DANN	Benign	0.66
PhyloP100		5.1

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: rs7648568;

hg19: chr3-137060689;