rs12331375

Positions:

• chr4-113810632-A-G
• chr4-113810632-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 0.27 in 151,988 control chromosomes in the GnomAD database, including 6,631 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 0.27 (6631 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.468 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: 0.270 AC: 41028 AN: 151874 Hom.: 6634 Cov.: 32

Gnomad AFR AF: 0.0959

Gnomad AMI AF: 0.261

Gnomad AMR AF: 0.310

Gnomad ASJ AF: 0.317

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.485

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.326

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.270 AC: 41031 AN: 151988 Hom.: 6631 Cov.: 32 AF XY: 0.274 AC XY: 20380 AN XY: 74282

Gnomad4 AFR AF: 0.0959

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.317

Gnomad4 EAS AF: 0.477

Gnomad4 SAS AF: 0.485

Gnomad4 FIN AF: 0.318

Gnomad4 NFE AF: 0.326

Gnomad4 OTH AF: 0.289

Alfa AF: 0.278 Hom.: 1049

Bravo AF: 0.258

Asia WGS AF: 0.456 AC: 1586 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.6
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12331375; hg19: chr4-114731788;