4-73689760-G-T

Variant names:

• chr4-73689760-G-T
• rs1358594

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 0.798 in 151,910 control chromosomes in the GnomAD database, including 51,439 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 0.80 (51439 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.447
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.934 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: 0.799 AC: 121253 AN: 151792 Hom.: 51434 Cov.: 31

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.933

Gnomad AMR AF: 0.894

Gnomad ASJ AF: 0.869

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.756

Gnomad FIN AF: 0.965

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.940

Gnomad OTH AF: 0.813

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

GnomAD4 genome AF: 0.798 AC: 121277 AN: 151910 Hom.: 51439 Cov.: 31 AF XY: 0.800 AC XY: 59372 AN XY: 74248

African (AFR) AF: 0.497 AC: 20517 AN: 41284

American (AMR) AF: 0.894 AC: 13628 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.869 AC: 3014 AN: 3470

East Asian (EAS) AF: 0.675 AC: 3485 AN: 5160

South Asian (SAS) AF: 0.756 AC: 3645 AN: 4824

European-Finnish (FIN) AF: 0.965 AC: 10245 AN: 10618

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.940 AC: 63945 AN: 68004

Other (OTH) AF: 0.808 AC: 1701 AN: 2106

Alfa AF: 0.888 Hom.: 188768

Bravo AF: 0.780

Asia WGS AF: 0.723 AC: 2515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.72
DANN	Benign	0.35
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs1358594; hg19: chr4-74555477;