19-40859445-A-T

Variant names:

• chr19-40859445-A-T
• rs7255616
• ENST00000601627.1:n.118-32546A>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000601627.1(ENSG00000268797):​n.118-32546A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0443 in 150,982 control chromosomes in the GnomAD database, including 405 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 0.044 (405 hom., cov: 31)
• Consequence: ENSG00000268797 ENST00000601627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.02

Genes affected

ENSG00000268797 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0627 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.118-32546A>T		intron_variant	Intron 1 of 3	3		ENSP00000469533.1

Frequencies

GnomAD3 genomes AF: 0.0443 AC: 6686 AN: 150866 Hom.: 404 Cov.: 31

Gnomad AFR AF: 0.0112

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0175

Gnomad ASJ AF: 0.0573

Gnomad EAS AF: 0.0326

Gnomad SAS AF: 0.0442

Gnomad FIN AF: 0.0906

Gnomad MID AF: 0.0478

Gnomad NFE AF: 0.0643

Gnomad OTH AF: 0.0371

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

GnomAD4 genome AF: 0.0443 AC: 6688 AN: 150982 Hom.: 405 Cov.: 31 AF XY: 0.0446 AC XY: 3282 AN XY: 73664

Gnomad4 AFR AF: 0.0112

Gnomad4 AMR AF: 0.0174

Gnomad4 ASJ AF: 0.0573

Gnomad4 EAS AF: 0.0327

Gnomad4 SAS AF: 0.0448

Gnomad4 FIN AF: 0.0906

Gnomad4 NFE AF: 0.0643

Gnomad4 OTH AF: 0.0368

Alfa AF: 0.0556 Hom.: 56

Bravo AF: 0.0379

Asia WGS AF: 0.0410 AC: 140 AN: 3428

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.35

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

Publications

LitVar

Other links and lift over

dbSNP: rs7255616; hg19: chr19-41365350;