chr7-128410652-C-A

Variant names:

• chr7-128410652-C-A
• rs72624928
• ENST00000784862.1:n.403-191G>T

Variant summary

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

The ENST00000784862.1(ENSG00000302195):​n.403-191G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.125 in 152,264 control chromosomes in the GnomAD database, including 1,240 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 0.13 (1240 hom., cov: 33)
• Consequence: ENSG00000302195 ENST00000784862.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.38
• Publications: 0 publications found

Genes affected

ENSG00000302195 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.139 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000784862.1. 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
	ENSG00000302195	ENST00000784862.1		n.403-191G>T		intron	N/A
	ENSG00000302195	ENST00000784863.1		n.*37G>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.125 AC: 19035 AN: 152146 Hom.: 1238 Cov.: 33

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.0975

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0300

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.150

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

GnomAD4 genome AF: 0.125 AC: 19049 AN: 152264 Hom.: 1240 Cov.: 33 AF XY: 0.121 AC XY: 9006 AN XY: 74448

African (AFR) AF: 0.142 AC: 5920 AN: 41548

American (AMR) AF: 0.0972 AC: 1488 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 515 AN: 3470

East Asian (EAS) AF: 0.000578 AC: 3 AN: 5188

South Asian (SAS) AF: 0.0302 AC: 146 AN: 4830

European-Finnish (FIN) AF: 0.122 AC: 1297 AN: 10596

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9174 AN: 68008

Other (OTH) AF: 0.148 AC: 313 AN: 2110

Alfa AF: 0.131 Hom.: 164

Bravo AF: 0.128

Asia WGS AF: 0.0270 AC: 93 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	13
DANN	Benign	0.66
PhyloP100		1.4
PromoterAI		-0.022	Neutral

Splicing

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

Other links and lift over

dbSNP: rs72624928; hg19: chr7-128050706;