19-49113981-A-G

Variant names:

• chr19-49113981-A-G
• rs4802562
• ENST00000750888.1:n.16-5384T>C

Variant summary

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

The ENST00000750888.1(ENSG00000297778):​n.16-5384T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 152,024 control chromosomes in the GnomAD database, including 11,702 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 0.39 (11702 hom., cov: 32)
• Consequence: ENSG00000297778 ENST00000750888.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.53
• Publications: 7 publications found

Genes affected

ENSG00000297778 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000750888.1. 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
	ENSG00000297778	ENST00000750888.1		n.16-5384T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.386 AC: 58595 AN: 151906 Hom.: 11679 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.379

Gnomad ASJ AF: 0.449

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.364

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.386 AC: 58659 AN: 152024 Hom.: 11702 Cov.: 32 AF XY: 0.379 AC XY: 28186 AN XY: 74300

African (AFR) AF: 0.466 AC: 19328 AN: 41452

American (AMR) AF: 0.379 AC: 5792 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.449 AC: 1556 AN: 3468

East Asian (EAS) AF: 0.216 AC: 1120 AN: 5174

South Asian (SAS) AF: 0.464 AC: 2236 AN: 4818

European-Finnish (FIN) AF: 0.254 AC: 2673 AN: 10544

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.364 AC: 24749 AN: 67976

Other (OTH) AF: 0.390 AC: 823 AN: 2110

Alfa AF: 0.379 Hom.: 6695

Bravo AF: 0.400

Asia WGS AF: 0.368 AC: 1282 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.80
DANN	Benign	0.46
PhyloP100		-2.5
PromoterAI		-0.025	Neutral

Splicing

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

Other links and lift over

dbSNP: rs4802562; hg19: chr19-49617238;