rs145379083

Variant names:

• chr4-63027560-G-A
• rs145379083

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 0.367 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.367 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

Gnomad4 AFR AF: 0.195

Gnomad4 AMR AF: 0.410

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.140

Gnomad4 SAS AF: 0.306

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.462

Gnomad4 OTH AF: 0.398

Alfa AF: 0.386 Hom.: 1557

Bravo AF: 0.349

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Publications

LitVar

Other links and lift over

dbSNP: rs145379083; hg19: chr4-63893278;