rs308393

Positions:

• chr4-122825464-A-C
• chr4-122825464-A-T

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 0.288 in 152,128 control chromosomes in the GnomAD database, including 9,704 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 0.29 (9704 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.608 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43769 AN: 152008 Hom.: 9667 Cov.: 32

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.117

Gnomad AMR AF: 0.239

Gnomad ASJ AF: 0.216

Gnomad EAS AF: 0.126

Gnomad SAS AF: 0.340

Gnomad FIN AF: 0.125

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.288 AC: 43864 AN: 152128 Hom.: 9704 Cov.: 32 AF XY: 0.286 AC XY: 21282 AN XY: 74378

Gnomad4 AFR AF: 0.615

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.216

Gnomad4 EAS AF: 0.126

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.125

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.275

Alfa AF: 0.207 Hom.: 677

Bravo AF: 0.309

Asia WGS AF: 0.305 AC: 1062 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	0.58
DANN	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs308393; hg19: chr4-123746619;