4-63651206-A-G

Variant names:

• chr4-63651206-A-G
• rs1004341

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 0.843 in 151,654 control chromosomes in the GnomAD database, including 56,688 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 0.84 (56688 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.79

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.843 AC: 127776 AN: 151536 Hom.: 56675 Cov.: 31

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.944

Gnomad AMR AF: 0.938

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.952

Gnomad FIN AF: 0.964

Gnomad MID AF: 0.927

Gnomad NFE AF: 0.965

Gnomad OTH AF: 0.888

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

GnomAD4 genome AF: 0.843 AC: 127831 AN: 151654 Hom.: 56688 Cov.: 31 AF XY: 0.846 AC XY: 62724 AN XY: 74100

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.938

Gnomad4 ASJ AF: 0.940

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.952

Gnomad4 FIN AF: 0.964

Gnomad4 NFE AF: 0.965

Gnomad4 OTH AF: 0.889

Alfa AF: 0.893 Hom.: 7764

Bravo AF: 0.828

Asia WGS AF: 0.956 AC: 3323 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.14
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1004341; hg19: chr4-64516924;