19-40835684-A-G

Variant names:

• chr19-40835684-A-G
• rs7251418
• ENST00000601627.1:n.117+34269A>G

Variant summary

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

The ENST00000601627.1(ENSG00000268797):​n.117+34269A>G variant causes a intron 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: ENSG00000268797 ENST00000601627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.956
• Publications: 14 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 (EAS) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000601627.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000268797	ENST00000601627.1	TSL:3	n.117+34269A>G		intron	N/A	ENSP00000469533.1
	ENSG00000269843	ENST00000596135.1	TSL:3	n.125+1402T>C		intron	N/A

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

African (AFR) AF: 0.790 AC: 32568 AN: 41218

American (AMR) AF: 0.761 AC: 11596 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2739 AN: 3470

East Asian (EAS) AF: 0.808 AC: 4180 AN: 5172

South Asian (SAS) AF: 0.657 AC: 3164 AN: 4818

European-Finnish (FIN) AF: 0.837 AC: 8828 AN: 10552

Middle Eastern (MID) AF: 0.714 AC: 207 AN: 290

European-Non Finnish (NFE) AF: 0.736 AC: 50014 AN: 67970

Other (OTH) AF: 0.752 AC: 1588 AN: 2112

Alfa AF: 0.738 Hom.: 117476

Bravo AF: 0.761

Asia WGS AF: 0.739 AC: 2569 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	2.2
DANN	Benign	0.74
PhyloP100		-0.96

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: rs7251418; hg19: chr19-41341589;