rs352054

Variant names:

• chr4-74015033-G-A
• rs352054

Your query was ambiguous. Multiple possible variants found:

• chr4-74015033-G-A
• chr4-74015033-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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;