rs4319121

Variant names:

• chr8-52593195-C-T
• rs4319121

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 0.233 in 152,080 control chromosomes in the GnomAD database, including 4,723 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 0.23 (4723 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.49
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.364 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: 0.233 AC: 35343 AN: 151962 Hom.: 4716 Cov.: 32

Gnomad AFR AF: 0.370

Gnomad AMI AF: 0.329

Gnomad AMR AF: 0.189

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.140

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.192

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.165

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.233 AC: 35379 AN: 152080 Hom.: 4723 Cov.: 32 AF XY: 0.235 AC XY: 17446 AN XY: 74348

African (AFR) AF: 0.369 AC: 15313 AN: 41456

American (AMR) AF: 0.189 AC: 2883 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 787 AN: 3472

East Asian (EAS) AF: 0.140 AC: 725 AN: 5168

South Asian (SAS) AF: 0.336 AC: 1618 AN: 4816

European-Finnish (FIN) AF: 0.192 AC: 2026 AN: 10578

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.165 AC: 11191 AN: 68006

Other (OTH) AF: 0.218 AC: 460 AN: 2112

Alfa AF: 0.187 Hom.: 5845

Bravo AF: 0.233

Asia WGS AF: 0.252 AC: 875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.3
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: rs4319121; hg19: chr8-53505755;