rs2319145

Variant names:

• chr4-167339525-C-G
• rs2319145

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 0.415 in 152,008 control chromosomes in the GnomAD database, including 13,828 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 0.42 (13828 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.409
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.48 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: 0.416 AC: 63136 AN: 151888 Hom.: 13836 Cov.: 32

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.286

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.485

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.415 AC: 63143 AN: 152008 Hom.: 13828 Cov.: 32 AF XY: 0.414 AC XY: 30800 AN XY: 74322

African (AFR) AF: 0.299 AC: 12372 AN: 41442

American (AMR) AF: 0.347 AC: 5306 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1739 AN: 3470

East Asian (EAS) AF: 0.287 AC: 1484 AN: 5176

South Asian (SAS) AF: 0.436 AC: 2100 AN: 4822

European-Finnish (FIN) AF: 0.553 AC: 5838 AN: 10550

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.485 AC: 32943 AN: 67964

Other (OTH) AF: 0.422 AC: 891 AN: 2112

Alfa AF: 0.456 Hom.: 2051

Bravo AF: 0.397

Asia WGS AF: 0.368 AC: 1280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.7
DANN	Benign	0.87
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs2319145; hg19: chr4-168260676;