rs4483064

chr7-35703475-G-Achr7-35703475-G-Cchr7-35703475-G-T

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 0.645 in 152,104 control chromosomes in the GnomAD database, including 32,855 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 0.65 (32855 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.818 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: 0.645 AC: 98026 AN: 151986 Hom.: 32817 Cov.: 32

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.659

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.629

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.531

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.556

Gnomad OTH AF: 0.634

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

GnomAD4 genome AF: 0.645 AC: 98124 AN: 152104 Hom.: 32855 Cov.: 32 AF XY: 0.644 AC XY: 47873 AN XY: 74336

Gnomad4 AFR AF: 0.825

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.629

Gnomad4 EAS AF: 0.730

Gnomad4 SAS AF: 0.679

Gnomad4 FIN AF: 0.531

Gnomad4 NFE AF: 0.556

Gnomad4 OTH AF: 0.636

Alfa AF: 0.601 Hom.: 5383

Bravo AF: 0.659

Asia WGS AF: 0.730 AC: 2537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.098
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4483064; hg19: chr7-35743085;