4-141470217-G-T

Variant names:

• chr4-141470217-G-T
• rs17354568

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 0.207 in 152,068 control chromosomes in the GnomAD database, including 3,438 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 (3438 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0400
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.257 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: 0.207 AC: 31495 AN: 151946 Hom.: 3427 Cov.: 32

Gnomad AFR AF: 0.257

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.264

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.220

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.217

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.207 AC: 31547 AN: 152068 Hom.: 3438 Cov.: 32 AF XY: 0.207 AC XY: 15394 AN XY: 74350

African (AFR) AF: 0.257 AC: 10667 AN: 41462

American (AMR) AF: 0.264 AC: 4036 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 639 AN: 3472

East Asian (EAS) AF: 0.220 AC: 1133 AN: 5160

South Asian (SAS) AF: 0.186 AC: 896 AN: 4816

European-Finnish (FIN) AF: 0.127 AC: 1347 AN: 10598

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.180 AC: 12254 AN: 67972

Other (OTH) AF: 0.202 AC: 424 AN: 2102

Alfa AF: 0.204 Hom.: 1413

Bravo AF: 0.219

Asia WGS AF: 0.212 AC: 740 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.0
DANN	Benign	0.22
PhyloP100		0.040

Splicing

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

Other links and lift over

dbSNP: rs17354568; hg19: chr4-142391371;