4-163320940-A-G

Variant names:

• chr4-163320940-A-G
• rs1574637

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 0.794 in 152,056 control chromosomes in the GnomAD database, including 50,439 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 0.79 (50439 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.365
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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: 0.794 AC: 120673 AN: 151938 Hom.: 50445 Cov.: 31

Gnomad AFR AF: 0.506

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.875

Gnomad ASJ AF: 0.867

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.912

Gnomad FIN AF: 0.918

Gnomad MID AF: 0.864

Gnomad NFE AF: 0.901

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.794 AC: 120702 AN: 152056 Hom.: 50439 Cov.: 31 AF XY: 0.799 AC XY: 59419 AN XY: 74324

African (AFR) AF: 0.506 AC: 20945 AN: 41408

American (AMR) AF: 0.875 AC: 13367 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.867 AC: 3009 AN: 3472

East Asian (EAS) AF: 0.994 AC: 5135 AN: 5168

South Asian (SAS) AF: 0.912 AC: 4390 AN: 4812

European-Finnish (FIN) AF: 0.918 AC: 9727 AN: 10596

Middle Eastern (MID) AF: 0.850 AC: 250 AN: 294

European-Non Finnish (NFE) AF: 0.901 AC: 61304 AN: 68012

Other (OTH) AF: 0.819 AC: 1729 AN: 2112

Alfa AF: 0.870 Hom.: 92963

Bravo AF: 0.779

Asia WGS AF: 0.884 AC: 3075 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.4
DANN	Benign	0.85
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs1574637; hg19: chr4-164242092;