chr19-40851439-T-C

Variant names:

• chr19-40851439-T-C
• rs4803381
• ENST00000601627.1:n.118-40552T>C

Variant summary

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

The ENST00000601627.1(ENSG00000268797):​n.118-40552T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.569 in 138,240 control chromosomes in the GnomAD database, including 21,385 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 0.57 (21385 hom., cov: 25)
• Consequence: ENSG00000268797 ENST00000601627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.136
• Publications: 17 publications found

Genes affected

ENSG00000268797 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.623 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
ENSG00000268797	ENST00000601627.1	n.118-40552T>C		intron_variant	Intron 1 of 3	3		ENSP00000469533.1

Frequencies

GnomAD3 genomes AF: 0.569 AC: 78637 AN: 138126 Hom.: 21370 Cov.: 25

Gnomad AFR AF: 0.477

Gnomad AMI AF: 0.676

Gnomad AMR AF: 0.634

Gnomad ASJ AF: 0.607

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.618

Gnomad MID AF: 0.578

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.567

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

GnomAD4 genome AF: 0.569 AC: 78683 AN: 138240 Hom.: 21385 Cov.: 25 AF XY: 0.567 AC XY: 38158 AN XY: 67290

African (AFR) AF: 0.476 AC: 18108 AN: 38032

American (AMR) AF: 0.635 AC: 8581 AN: 13522

Ashkenazi Jewish (ASJ) AF: 0.607 AC: 1976 AN: 3254

East Asian (EAS) AF: 0.505 AC: 2236 AN: 4432

South Asian (SAS) AF: 0.496 AC: 2109 AN: 4250

European-Finnish (FIN) AF: 0.618 AC: 5631 AN: 9108

Middle Eastern (MID) AF: 0.576 AC: 160 AN: 278

European-Non Finnish (NFE) AF: 0.611 AC: 38280 AN: 62690

Other (OTH) AF: 0.565 AC: 1049 AN: 1856

Alfa AF: 0.614 Hom.: 7802

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.6
DANN	Benign	0.28
PhyloP100		-0.14

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: rs4803381; hg19: chr19-41357344;