rs12899331

Variant names:

• chr15-55508896-A-G
• rs12899331

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The variant allele was found at a frequency of 0.187 in 152,116 control chromosomes in the GnomAD database, including 3,206 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.19 (3206 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.149

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BP6: Variant 15-55508896-A-G is Benign according to our data. Variant chr15-55508896-A-G is described in ClinVar as [Benign]. Clinvar id is 1168574.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.25 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: 0.187 AC: 28400 AN: 151998 Hom.: 3207 Cov.: 32

Gnomad AFR AF: 0.0586

Gnomad AMI AF: 0.224

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.347

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.205

Gnomad FIN AF: 0.183

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.220

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

GnomAD4 genome AF: 0.187 AC: 28395 AN: 152116 Hom.: 3206 Cov.: 32 AF XY: 0.184 AC XY: 13691 AN XY: 74364

Gnomad4 AFR AF: 0.0585

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.347

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.206

Gnomad4 FIN AF: 0.183

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.218

Alfa AF: 0.224 Hom.: 1130

Bravo AF: 0.181

Asia WGS AF: 0.173 AC: 603 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Jan 23, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	5.4
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12899331; hg19: chr15-55801094;