4-17219610-C-T

Variant names:

• chr4-17219610-C-T
• rs12643440

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 0.211 in 152,116 control chromosomes in the GnomAD database, including 3,951 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 0.21 (3951 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.269 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: 0.212 AC: 32179 AN: 151998 Hom.: 3955 Cov.: 32

Gnomad AFR AF: 0.0847

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.233

Gnomad ASJ AF: 0.271

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.214

Gnomad FIN AF: 0.244

Gnomad MID AF: 0.232

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.225

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

GnomAD4 genome AF: 0.211 AC: 32165 AN: 152116 Hom.: 3951 Cov.: 32 AF XY: 0.210 AC XY: 15603 AN XY: 74352

African (AFR) AF: 0.0845 AC: 3508 AN: 41504

American (AMR) AF: 0.233 AC: 3551 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.271 AC: 942 AN: 3472

East Asian (EAS) AF: 0.254 AC: 1312 AN: 5168

South Asian (SAS) AF: 0.213 AC: 1028 AN: 4826

European-Finnish (FIN) AF: 0.244 AC: 2587 AN: 10584

Middle Eastern (MID) AF: 0.233 AC: 68 AN: 292

European-Non Finnish (NFE) AF: 0.272 AC: 18499 AN: 67978

Other (OTH) AF: 0.224 AC: 473 AN: 2114

Alfa AF: 0.226 Hom.: 2291

Bravo AF: 0.206

Asia WGS AF: 0.256 AC: 888 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.25
DANN	Benign	0.56
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs12643440; hg19: chr4-17221233;