rs2855475

Variant names:

• chr16-31136227-G-A
• rs2855475

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 0.618 in 152,066 control chromosomes in the GnomAD database, including 29,985 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 0.62 (29985 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0530

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.803 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: 0.618 AC: 93870 AN: 151948 Hom.: 29950 Cov.: 32

Gnomad AFR AF: 0.660

Gnomad AMI AF: 0.565

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.459

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.823

Gnomad FIN AF: 0.610

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.634

Gnomad OTH AF: 0.579

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

GnomAD4 genome AF: 0.618 AC: 93960 AN: 152066 Hom.: 29985 Cov.: 32 AF XY: 0.617 AC XY: 45891 AN XY: 74348

Gnomad4 AFR AF: 0.660

Gnomad4 AMR AF: 0.590

Gnomad4 ASJ AF: 0.459

Gnomad4 EAS AF: 0.108

Gnomad4 SAS AF: 0.824

Gnomad4 FIN AF: 0.610

Gnomad4 NFE AF: 0.634

Gnomad4 OTH AF: 0.580

Alfa AF: 0.622 Hom.: 18759

Bravo AF: 0.604

Asia WGS AF: 0.523 AC: 1815 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	1.3
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2855475; hg19: chr16-31147548;