rs1425658

Positions:

• chr4-67198813-A-C
• chr4-67198813-A-G

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 0.781 in 152,156 control chromosomes in the GnomAD database, including 47,059 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 0.78 (47059 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.958 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: 0.781 AC: 118675 AN: 152038 Hom.: 46990 Cov.: 32

Gnomad AFR AF: 0.883

Gnomad AMI AF: 0.767

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.981

Gnomad SAS AF: 0.900

Gnomad FIN AF: 0.679

Gnomad MID AF: 0.709

Gnomad NFE AF: 0.708

Gnomad OTH AF: 0.755

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

GnomAD4 genome AF: 0.781 AC: 118804 AN: 152156 Hom.: 47059 Cov.: 32 AF XY: 0.782 AC XY: 58157 AN XY: 74362

Gnomad4 AFR AF: 0.883

Gnomad4 AMR AF: 0.820

Gnomad4 ASJ AF: 0.676

Gnomad4 EAS AF: 0.981

Gnomad4 SAS AF: 0.900

Gnomad4 FIN AF: 0.679

Gnomad4 NFE AF: 0.708

Gnomad4 OTH AF: 0.759

Alfa AF: 0.723 Hom.: 55598

Bravo AF: 0.793

Asia WGS AF: 0.930 AC: 3228 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	0.95
DANN	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1425658; hg19: chr4-68064531;