7-128410893-G-T

Variant names:

• chr7-128410893-G-T
• rs72624924
• ENST00000784863.1:n.743C>A

Variant summary

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

The ENST00000784863.1(ENSG00000302195):​n.743C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0775 in 152,058 control chromosomes in the GnomAD database, including 677 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 0.077 (677 hom., cov: 33)
• Consequence: ENSG00000302195 ENST00000784863.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.26
• 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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302195	ENST00000784863.1	n.743C>A		non_coding_transcript_exon_variant	Exon 3 of 3
ENSG00000302195	ENST00000784862.1	n.403-432C>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0775 AC: 11772 AN: 151940 Hom.: 674 Cov.: 33

Gnomad AFR AF: 0.113

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.0574

Gnomad ASJ AF: 0.0908

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.138

Gnomad FIN AF: 0.0132

Gnomad MID AF: 0.0823

Gnomad NFE AF: 0.0506

Gnomad OTH AF: 0.0864

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

GnomAD4 genome AF: 0.0775 AC: 11784 AN: 152058 Hom.: 677 Cov.: 33 AF XY: 0.0777 AC XY: 5775 AN XY: 74362

African (AFR) AF: 0.113 AC: 4676 AN: 41448

American (AMR) AF: 0.0573 AC: 875 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0908 AC: 315 AN: 3470

East Asian (EAS) AF: 0.273 AC: 1409 AN: 5154

South Asian (SAS) AF: 0.137 AC: 663 AN: 4824

European-Finnish (FIN) AF: 0.0132 AC: 140 AN: 10596

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0506 AC: 3437 AN: 67982

Other (OTH) AF: 0.0859 AC: 181 AN: 2106

Alfa AF: 0.0166 Hom.: 10

Bravo AF: 0.0817

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.58
DANN	Benign	0.25
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs72624924; hg19: chr7-128050947; COSMIC: COSV58314997;