rs1496402

chr19-40860229-T-Achr19-40860229-T-C

Variant summary

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

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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;