7-1512784-G-A

Variant names:

• chr7-1512784-G-A
• rs6942930
• ENST00000728231.1:n.157-5428G>A

Variant summary

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

The ENST00000728231.1(ENSG00000295143):​n.157-5428G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 151,830 control chromosomes in the GnomAD database, including 18,923 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 0.50 (18923 hom., cov: 33)
• Consequence: ENSG00000295143 ENST00000728231.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 11 publications found

Genes affected

ENSG00000295143 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000728231.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000295143	ENST00000728231.1		n.157-5428G>A		intron	N/A
	ENSG00000295143	ENST00000728232.1		n.107+2252G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75507 AN: 151710 Hom.: 18923 Cov.: 33

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.673

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.641

Gnomad SAS AF: 0.538

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.491

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.498 AC: 75547 AN: 151830 Hom.: 18923 Cov.: 33 AF XY: 0.500 AC XY: 37109 AN XY: 74202

African (AFR) AF: 0.477 AC: 19774 AN: 41448

American (AMR) AF: 0.477 AC: 7283 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.405 AC: 1405 AN: 3468

East Asian (EAS) AF: 0.640 AC: 3271 AN: 5110

South Asian (SAS) AF: 0.536 AC: 2585 AN: 4820

European-Finnish (FIN) AF: 0.575 AC: 6057 AN: 10538

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.491 AC: 33336 AN: 67866

Other (OTH) AF: 0.506 AC: 1067 AN: 2108

Alfa AF: 0.494 Hom.: 8598

Bravo AF: 0.489

Asia WGS AF: 0.575 AC: 1999 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.2
DANN	Benign	0.67
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs6942930; hg19: chr7-1552420;