rs145379083

Positions:

• chr4-63027560-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;