19-7510522-A-G

Variant names:

• chr19-7510522-A-G
• rs4804662
• ENST00000599312.1:c.60+3381A>G

Variant summary

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

The ENST00000599312.1(ENSG00000267952):​c.60+3381A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.232 in 152,166 control chromosomes in the GnomAD database, including 4,479 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 0.23 (4479 hom., cov: 32)
• Consequence: ENSG00000267952 ENST00000599312.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316
• Publications: 4 publications found

Genes affected

ENSG00000267952 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000599312.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000267952	ENST00000599312.1	TSL:2	c.60+3381A>G		intron	N/A	ENSP00000469588.1	M0QY47
	ENSG00000267952	ENST00000597384.1	TSL:3	n.91-3358A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.232 AC: 35305 AN: 152048 Hom.: 4466 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.269

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.232 AC: 35347 AN: 152166 Hom.: 4479 Cov.: 32 AF XY: 0.233 AC XY: 17320 AN XY: 74386

African (AFR) AF: 0.138 AC: 5717 AN: 41524

American (AMR) AF: 0.281 AC: 4289 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 689 AN: 3470

East Asian (EAS) AF: 0.259 AC: 1340 AN: 5174

South Asian (SAS) AF: 0.234 AC: 1129 AN: 4820

European-Finnish (FIN) AF: 0.297 AC: 3146 AN: 10604

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.269 AC: 18300 AN: 67986

Other (OTH) AF: 0.229 AC: 483 AN: 2110

Alfa AF: 0.256 Hom.: 10962

Bravo AF: 0.227

Asia WGS AF: 0.268 AC: 931 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	2.5
DANN	Benign	0.83
PhyloP100		-0.32

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs4804662; hg19: chr19-7575408;