4-63027560-G-A

Variant names:

• chr4-63027560-G-A
• rs145379083

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 0.367 in 146,134 control chromosomes in the GnomAD database, including 11,082 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 0.37 (11082 hom., cov: 27)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.457 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.367 AC: 53600 AN: 146048 Hom.: 11083 Cov.: 27

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.307

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.462

Gnomad OTH AF: 0.402

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

GnomAD4 genome AF: 0.367 AC: 53591 AN: 146134 Hom.: 11082 Cov.: 27 AF XY: 0.364 AC XY: 25828 AN XY: 70902

African (AFR) AF: 0.195 AC: 7677 AN: 39362

American (AMR) AF: 0.410 AC: 5923 AN: 14430

Ashkenazi Jewish (ASJ) AF: 0.440 AC: 1503 AN: 3416

East Asian (EAS) AF: 0.140 AC: 708 AN: 5068

South Asian (SAS) AF: 0.306 AC: 1396 AN: 4566

European-Finnish (FIN) AF: 0.455 AC: 4508 AN: 9918

Middle Eastern (MID) AF: 0.514 AC: 146 AN: 284

European-Non Finnish (NFE) AF: 0.462 AC: 30557 AN: 66206

Other (OTH) AF: 0.398 AC: 795 AN: 1998

Alfa AF: 0.227 Hom.: 1557

Bravo AF: 0.349

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.2
DANN	Benign	0.80

Splicing

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

Other links and lift over

dbSNP: rs145379083; hg19: chr4-63893278;