rs352054

chr4-74015033-G-Achr4-74015033-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.927 in 152,208 control chromosomes in the GnomAD database, including 65,502 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 0.93 (65502 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0800

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.927 AC: 140945 AN: 152090 Hom.: 65461 Cov.: 31

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.894

Gnomad AMR AF: 0.937

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.948

Gnomad SAS AF: 0.911

Gnomad FIN AF: 0.962

Gnomad MID AF: 0.851

Gnomad NFE AF: 0.963

Gnomad OTH AF: 0.925

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

GnomAD4 genome AF: 0.927 AC: 141042 AN: 152208 Hom.: 65502 Cov.: 31 AF XY: 0.925 AC XY: 68838 AN XY: 74422

Gnomad4 AFR AF: 0.857

Gnomad4 AMR AF: 0.937

Gnomad4 ASJ AF: 0.899

Gnomad4 EAS AF: 0.948

Gnomad4 SAS AF: 0.912

Gnomad4 FIN AF: 0.962

Gnomad4 NFE AF: 0.963

Gnomad4 OTH AF: 0.924

Alfa AF: 0.942 Hom.: 14964

Bravo AF: 0.922

Asia WGS AF: 0.895 AC: 3112 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.9
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs352054; hg19: chr4-74880750;