19-43782508-T-C

Variant names:

• chr19-43782508-T-C
• rs3760983
• ENST00000765554.1:n.514A>G

Variant summary

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

The ENST00000765554.1(ENSG00000299675):​n.514A>G 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 0.556 in 151,838 control chromosomes in the GnomAD database, including 23,967 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 0.56 (23967 hom., cov: 31)
• Consequence: ENSG00000299675 ENST00000765554.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11
• Publications: 23 publications found

Genes affected

ENSG00000299675 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000765554.1. 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
	ENSG00000299675	ENST00000765554.1		n.514A>G		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84295 AN: 151720 Hom.: 23939 Cov.: 31

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.433

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.534

Gnomad OTH AF: 0.552

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

GnomAD4 genome AF: 0.556 AC: 84372 AN: 151838 Hom.: 23967 Cov.: 31 AF XY: 0.561 AC XY: 41608 AN XY: 74174

African (AFR) AF: 0.524 AC: 21690 AN: 41380

American (AMR) AF: 0.658 AC: 10043 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1986 AN: 3468

East Asian (EAS) AF: 0.842 AC: 4329 AN: 5142

South Asian (SAS) AF: 0.432 AC: 2076 AN: 4804

European-Finnish (FIN) AF: 0.582 AC: 6133 AN: 10536

Middle Eastern (MID) AF: 0.507 AC: 149 AN: 294

European-Non Finnish (NFE) AF: 0.534 AC: 36295 AN: 67932

Other (OTH) AF: 0.552 AC: 1163 AN: 2108

Alfa AF: 0.549 Hom.: 41884

Bravo AF: 0.564

Asia WGS AF: 0.604 AC: 2097 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.25
DANN	Benign	0.33
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs3760983; hg19: chr19-44286660;