19-24172691-G-C

Variant names:

• chr19-24172691-G-C
• rs11668609

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 0.317 in 152,046 control chromosomes in the GnomAD database, including 9,424 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 0.32 (9424 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.82
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.553 is higher than 0.05.

Variant Effect in Transcripts

 

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

Frequencies

GnomAD3 genomes AF: 0.316 AC: 48046 AN: 151928 Hom.: 9379 Cov.: 33

Gnomad AFR AF: 0.558

Gnomad AMI AF: 0.235

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.253

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.213

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.317 AC: 48145 AN: 152046 Hom.: 9424 Cov.: 33 AF XY: 0.313 AC XY: 23282 AN XY: 74314

African (AFR) AF: 0.559 AC: 23187 AN: 41468

American (AMR) AF: 0.262 AC: 4003 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 600 AN: 3470

East Asian (EAS) AF: 0.252 AC: 1302 AN: 5166

South Asian (SAS) AF: 0.240 AC: 1156 AN: 4818

European-Finnish (FIN) AF: 0.240 AC: 2529 AN: 10556

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.213 AC: 14488 AN: 67976

Other (OTH) AF: 0.275 AC: 580 AN: 2108

Alfa AF: 0.130 Hom.: 208

Bravo AF: 0.330

Asia WGS AF: 0.273 AC: 952 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	2.9
DANN	Benign	0.45
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs11668609; hg19: chr19-24355493;