rs12899331

Variant names:

• chr15-55508896-A-G
• rs12899331

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

ACMG classification

Our verdict: Benign. The variant received -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 VariationId 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

African (AFR) AF: 0.0585 AC: 2427 AN: 41516

American (AMR) AF: 0.209 AC: 3199 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.347 AC: 1203 AN: 3468

East Asian (EAS) AF: 0.137 AC: 704 AN: 5148

South Asian (SAS) AF: 0.206 AC: 993 AN: 4828

European-Finnish (FIN) AF: 0.183 AC: 1933 AN: 10588

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.253 AC: 17181 AN: 67984

Other (OTH) AF: 0.218 AC: 458 AN: 2104

Alfa AF: 0.220 Hom.: 1773

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

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	5.4
DANN	Benign	0.78
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs12899331; hg19: chr15-55801094;