chr4-63651206-A-G

Variant names:

• chr4-63651206-A-G
• rs1004341

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 0.843 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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.531 AC: 21979 AN: 41368

American (AMR) AF: 0.938 AC: 14214 AN: 15152

Ashkenazi Jewish (ASJ) AF: 0.940 AC: 3255 AN: 3462

East Asian (EAS) AF: 0.999 AC: 5106 AN: 5110

South Asian (SAS) AF: 0.952 AC: 4583 AN: 4812

European-Finnish (FIN) AF: 0.964 AC: 10229 AN: 10614

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.965 AC: 65457 AN: 67822

Other (OTH) AF: 0.889 AC: 1875 AN: 2108

Alfa AF: 0.877 Hom.: 7869

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
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs1004341; hg19: chr4-64516924;