chr4-167850337-A-G

Variant names:

• chr4-167850337-A-G
• rs9312225

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 0.493 in 151,948 control chromosomes in the GnomAD database, including 19,738 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 0.49 (19738 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.43
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.657 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: 0.492 AC: 74767 AN: 151830 Hom.: 19724 Cov.: 32

Gnomad AFR AF: 0.664

Gnomad AMI AF: 0.429

Gnomad AMR AF: 0.429

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.388

Gnomad FIN AF: 0.423

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.504

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

GnomAD4 genome AF: 0.493 AC: 74840 AN: 151948 Hom.: 19738 Cov.: 32 AF XY: 0.486 AC XY: 36068 AN XY: 74234

African (AFR) AF: 0.664 AC: 27508 AN: 41426

American (AMR) AF: 0.429 AC: 6551 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1448 AN: 3470

East Asian (EAS) AF: 0.126 AC: 653 AN: 5176

South Asian (SAS) AF: 0.389 AC: 1876 AN: 4824

European-Finnish (FIN) AF: 0.423 AC: 4454 AN: 10530

Middle Eastern (MID) AF: 0.592 AC: 173 AN: 292

European-Non Finnish (NFE) AF: 0.452 AC: 30735 AN: 67952

Other (OTH) AF: 0.498 AC: 1051 AN: 2110

Alfa AF: 0.464 Hom.: 5761

Bravo AF: 0.504

Asia WGS AF: 0.293 AC: 1020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	18
DANN	Benign	0.80
PhyloP100		2.4

Splicing

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

Other links and lift over

dbSNP: rs9312225; hg19: chr4-168771488;