chr19-7739629-A-G

Variant names:

• chr19-7739629-A-G
• rs8112555
• ENST00000678003.1:n.*290+1938T>C

Variant summary

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

The ENST00000678003.1(ENSG00000288669):​n.*290+1938T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 151,644 control chromosomes in the GnomAD database, including 43,274 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 0.74 (43274 hom., cov: 31)
• Consequence: ENSG00000288669 ENST00000678003.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.918
• Publications: 1 publications found

Genes affected

ENSG00000288669 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.842 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000678003.1. 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
	ENSG00000288669	ENST00000678003.1		n.*290+1938T>C		intron	N/A	ENSP00000504497.1
	ENSG00000288669	ENST00000676543.1		n.71-5655T>C		intron	N/A	ENSP00000503143.1
	ENSG00000288669	ENST00000678227.1		n.579+1938T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.740 AC: 112062 AN: 151524 Hom.: 43257 Cov.: 31

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.808

Gnomad ASJ AF: 0.845

Gnomad EAS AF: 0.679

Gnomad SAS AF: 0.787

Gnomad FIN AF: 0.880

Gnomad MID AF: 0.844

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.739 AC: 112115 AN: 151644 Hom.: 43274 Cov.: 31 AF XY: 0.741 AC XY: 54906 AN XY: 74120

African (AFR) AF: 0.489 AC: 20233 AN: 41354

American (AMR) AF: 0.809 AC: 12322 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.845 AC: 2925 AN: 3460

East Asian (EAS) AF: 0.680 AC: 3486 AN: 5130

South Asian (SAS) AF: 0.789 AC: 3792 AN: 4808

European-Finnish (FIN) AF: 0.880 AC: 9253 AN: 10512

Middle Eastern (MID) AF: 0.837 AC: 241 AN: 288

European-Non Finnish (NFE) AF: 0.848 AC: 57511 AN: 67842

Other (OTH) AF: 0.779 AC: 1644 AN: 2110

Alfa AF: 0.788 Hom.: 6048

Bravo AF: 0.725

Asia WGS AF: 0.735 AC: 2556 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.061
DANN	Benign	0.35
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs8112555; hg19: chr19-7804515;