19-40835684-A-G

Position:

• chr19-40835684-A-G

Variant summary

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

The ENST00000596135.1(ENSG00000269843):​n.125+1402T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 151,754 control chromosomes in the GnomAD database, including 44,093 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 0.76 (44093 hom., cov: 31)
• Consequence: ENST00000596135.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.956

Genes affected

(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 (EAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000596135.1	n.125+1402T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.761 AC: 115410 AN: 151636 Hom.: 44046 Cov.: 31

Gnomad AFR AF: 0.790

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.808

Gnomad SAS AF: 0.658

Gnomad FIN AF: 0.837

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.736

Gnomad OTH AF: 0.753

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

GnomAD4 genome AF: 0.761 AC: 115513 AN: 151754 Hom.: 44093 Cov.: 31 AF XY: 0.762 AC XY: 56542 AN XY: 74196

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.761

Gnomad4 ASJ AF: 0.789

Gnomad4 EAS AF: 0.808

Gnomad4 SAS AF: 0.657

Gnomad4 FIN AF: 0.837

Gnomad4 NFE AF: 0.736

Gnomad4 OTH AF: 0.752

Alfa AF: 0.733 Hom.: 77835

Bravo AF: 0.761

Asia WGS AF: 0.739 AC: 2569 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.74

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: rs7251418; hg19: chr19-41341589;