chr2-19368674-C-A

Variant names:

• chr2-19368674-C-A
• rs17441606

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.237 in 152,174 control chromosomes in the GnomAD database, including 4,795 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 0.24 (4795 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.19
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.26).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.308 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

Frequencies

GnomAD3 genomes AF: 0.237 AC: 36041 AN: 152056 Hom.: 4797 Cov.: 33

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.209

Gnomad EAS AF: 0.0329

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.237 AC: 36036 AN: 152174 Hom.: 4795 Cov.: 33 AF XY: 0.230 AC XY: 17090 AN XY: 74394

African (AFR) AF: 0.164 AC: 6811 AN: 41534

American (AMR) AF: 0.186 AC: 2839 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.209 AC: 724 AN: 3470

East Asian (EAS) AF: 0.0328 AC: 170 AN: 5182

South Asian (SAS) AF: 0.201 AC: 968 AN: 4812

European-Finnish (FIN) AF: 0.221 AC: 2339 AN: 10590

Middle Eastern (MID) AF: 0.209 AC: 61 AN: 292

European-Non Finnish (NFE) AF: 0.312 AC: 21207 AN: 67978

Other (OTH) AF: 0.233 AC: 492 AN: 2110

Alfa AF: 0.277 Hom.: 10220

Bravo AF: 0.233

Asia WGS AF: 0.112 AC: 391 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.26
CADD	Uncertain	24
DANN	Benign	0.60
PhyloP100		2.2

Splicing

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

Other links and lift over

dbSNP: rs17441606; hg19: chr2-19568435;