ENST00000787994.1:n.760+1998G>A

Variant names:

• chr7-127623832-G-A
• rs7801118
• ENST00000787994.1:n.760+1998G>A

Variant summary

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

The ENST00000787994.1(ENSG00000302590):​n.760+1998G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 152,030 control chromosomes in the GnomAD database, including 4,062 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 0.22 (4062 hom., cov: 32)
• Consequence: ENSG00000302590 ENST00000787994.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.450
• Publications: 5 publications found

Genes affected

ENSG00000302590 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000787994.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302590	ENST00000787994.1		n.760+1998G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33293 AN: 151912 Hom.: 4048 Cov.: 32

Gnomad AFR AF: 0.328

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.262

Gnomad FIN AF: 0.210

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.177

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.219 AC: 33336 AN: 152030 Hom.: 4062 Cov.: 32 AF XY: 0.220 AC XY: 16381 AN XY: 74316

African (AFR) AF: 0.328 AC: 13583 AN: 41444

American (AMR) AF: 0.169 AC: 2579 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.138 AC: 478 AN: 3472

East Asian (EAS) AF: 0.124 AC: 644 AN: 5184

South Asian (SAS) AF: 0.261 AC: 1258 AN: 4814

European-Finnish (FIN) AF: 0.210 AC: 2212 AN: 10546

Middle Eastern (MID) AF: 0.116 AC: 34 AN: 294

European-Non Finnish (NFE) AF: 0.177 AC: 12033 AN: 67976

Other (OTH) AF: 0.194 AC: 409 AN: 2110

Alfa AF: 0.197 Hom.: 1158

Bravo AF: 0.218

Asia WGS AF: 0.176 AC: 615 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.9
DANN	Benign	0.59
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs7801118; hg19: chr7-127263886;