rs17620029

chr19-24171510-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 0.134 in 152,118 control chromosomes in the GnomAD database, including 1,423 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 0.13 (1423 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.156 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: 0.134 AC: 20412 AN: 151998 Hom.: 1423 Cov.: 32

Gnomad AFR AF: 0.104

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0919

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.153

Gnomad NFE AF: 0.153

Gnomad OTH AF: 0.109

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

GnomAD4 genome AF: 0.134 AC: 20417 AN: 152118 Hom.: 1423 Cov.: 32 AF XY: 0.134 AC XY: 9942 AN XY: 74366

Gnomad4 AFR AF: 0.104

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.0919

Gnomad4 EAS AF: 0.166

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.153

Gnomad4 OTH AF: 0.108

Alfa AF: 0.142 Hom.: 2057

Bravo AF: 0.128

Asia WGS AF: 0.154 AC: 537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	0.65
Dann	Benign	0.87

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs17620029; hg19: chr19-24354312;