rs1496402

Variant names:

• chr19-40860229-T-A
• rs1496402
• ENST00000601627.1:n.118-31762T>A

Your query was ambiguous. Multiple possible variants found:

• chr19-40860229-T-A
• chr19-40860229-T-C

Variant summary

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

The ENST00000601627.1(ENSG00000268797):​n.118-31762T>A variant causes a intron change. The variant allele was found at a frequency of 0.663 in 150,500 control chromosomes in the GnomAD database, including 34,091 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 (34091 hom., cov: 30)
• Consequence: ENSG00000268797 ENST00000601627.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

Genes affected

ENSG00000268797 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.703 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.118-31762T>A		intron_variant	Intron 1 of 3	3		ENSP00000469533.1

Frequencies

GnomAD3 genomes AF: 0.663 AC: 99764 AN: 150386 Hom.: 34057 Cov.: 30

Gnomad AFR AF: 0.661

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.714

Gnomad ASJ AF: 0.645

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.702

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.663

Gnomad OTH AF: 0.652

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

GnomAD4 genome AF: 0.663 AC: 99836 AN: 150500 Hom.: 34091 Cov.: 30 AF XY: 0.661 AC XY: 48491 AN XY: 73412

Gnomad4 AFR AF: 0.661

Gnomad4 AMR AF: 0.714

Gnomad4 ASJ AF: 0.645

Gnomad4 EAS AF: 0.555

Gnomad4 SAS AF: 0.561

Gnomad4 FIN AF: 0.702

Gnomad4 NFE AF: 0.663

Gnomad4 OTH AF: 0.651

Alfa AF: 0.669 Hom.: 4365

Bravo AF: 0.667

Asia WGS AF: 0.568 AC: 1948 AN: 3428

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.5
DANN	Benign	0.40

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: rs1496402; hg19: chr19-41366134;