rs12899331

chr15-55508896-A-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 29, 2024

- -

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;