19-40835845-A-G

Variant names:

• chr19-40835845-A-G
• rs7251570
• ENST00000601627.1:n.117+34430A>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+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
• Publications: 2 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=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.664 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+34430A>G		intron	N/A	ENSP00000469533.1
	ENSG00000269843	ENST00000596135.1	TSL:3	n.125+1241T>C		intron	N/A

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

African (AFR) AF: 0.670 AC: 27625 AN: 41224

American (AMR) AF: 0.660 AC: 10066 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.708 AC: 2452 AN: 3464

East Asian (EAS) AF: 0.455 AC: 2345 AN: 5156

South Asian (SAS) AF: 0.516 AC: 2491 AN: 4824

European-Finnish (FIN) AF: 0.725 AC: 7667 AN: 10582

Middle Eastern (MID) AF: 0.636 AC: 187 AN: 294

European-Non Finnish (NFE) AF: 0.667 AC: 45364 AN: 67972

Other (OTH) AF: 0.652 AC: 1370 AN: 2100

Alfa AF: 0.667 Hom.: 5777

Bravo AF: 0.658

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.51
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: rs7251570; hg19: chr19-41341750;