rs308393

Variant names:

• chr4-122825464-A-C
• rs308393

Your query was ambiguous. Multiple possible variants found:

• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;