19-40835845-A-G

Position:

• chr19-40835845-A-G

Variant summary

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

The ENST00000601627.1(ENSG00000268797):​n.117+34430A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 151,790 control chromosomes in the GnomAD database, including 33,293 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 0.66 (33293 hom., cov: 32)
• Consequence: ENSG00000268797 ENST00000601627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.956

Genes affected

ENSG00000268797 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.664 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
ENSG00000268797	ENST00000601627.1	n.117+34430A>G		intron_variant		3		ENSP00000469533.1
ENSG00000269843	ENST00000596135.1	n.125+1241T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.660 AC: 100079 AN: 151672 Hom.: 33258 Cov.: 32

Gnomad AFR AF: 0.670

Gnomad AMI AF: 0.663

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.708

Gnomad EAS AF: 0.454

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.725

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.667

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.660 AC: 100172 AN: 151790 Hom.: 33293 Cov.: 32 AF XY: 0.657 AC XY: 48793 AN XY: 74224

Gnomad4 AFR AF: 0.670

Gnomad4 AMR AF: 0.660

Gnomad4 ASJ AF: 0.708

Gnomad4 EAS AF: 0.455

Gnomad4 SAS AF: 0.516

Gnomad4 FIN AF: 0.725

Gnomad4 NFE AF: 0.667

Gnomad4 OTH AF: 0.652

Alfa AF: 0.667 Hom.: 5777

Bravo AF: 0.658

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.51

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: rs7251570; hg19: chr19-41341750;