rs17620029

Variant names:

• chr19-24171510-T-C
• rs17620029

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.104 AC: 4301 AN: 41516

American (AMR) AF: 0.102 AC: 1559 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0919 AC: 319 AN: 3470

East Asian (EAS) AF: 0.166 AC: 855 AN: 5160

South Asian (SAS) AF: 0.144 AC: 694 AN: 4810

European-Finnish (FIN) AF: 0.177 AC: 1865 AN: 10552

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.153 AC: 10376 AN: 68000

Other (OTH) AF: 0.108 AC: 229 AN: 2114

Alfa AF: 0.141 Hom.: 2432

Bravo AF: 0.128

Asia WGS AF: 0.154 AC: 537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	0.65
DANN	Benign	0.87
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs17620029; hg19: chr19-24354312;