19-43782361-A-G

Variant names:

• chr19-43782361-A-G
• rs3760982
• ENST00000765554.1:n.661T>C

Variant summary

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

The ENST00000765554.1(ENSG00000299675):​n.661T>C 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 151,976 control chromosomes in the GnomAD database, including 24,014 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 (24014 hom., cov: 32)
• Consequence: ENSG00000299675 ENST00000765554.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168
• Publications: 89 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.821 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299675	ENST00000765554.1	n.661T>C		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.556 AC: 84434 AN: 151858 Hom.: 23986 Cov.: 32

Gnomad AFR AF: 0.525

Gnomad AMI AF: 0.559

Gnomad AMR AF: 0.657

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.435

Gnomad FIN AF: 0.584

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: 84511 AN: 151976 Hom.: 24014 Cov.: 32 AF XY: 0.562 AC XY: 41709 AN XY: 74276

African (AFR) AF: 0.525 AC: 21740 AN: 41406

American (AMR) AF: 0.657 AC: 10040 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1985 AN: 3466

East Asian (EAS) AF: 0.842 AC: 4356 AN: 5176

South Asian (SAS) AF: 0.434 AC: 2092 AN: 4818

European-Finnish (FIN) AF: 0.584 AC: 6166 AN: 10566

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

European-Non Finnish (NFE) AF: 0.534 AC: 36309 AN: 67958

Other (OTH) AF: 0.552 AC: 1165 AN: 2112

Alfa AF: 0.543 Hom.: 96235

Bravo AF: 0.565

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.49
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs3760982; hg19: chr19-44286513;