chr16-31136227-G-A

Variant names:

• chr16-31136227-G-A
• rs2855475

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 32 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.660 AC: 27367 AN: 41440

American (AMR) AF: 0.590 AC: 9011 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.459 AC: 1593 AN: 3472

East Asian (EAS) AF: 0.108 AC: 561 AN: 5180

South Asian (SAS) AF: 0.824 AC: 3983 AN: 4834

European-Finnish (FIN) AF: 0.610 AC: 6457 AN: 10580

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.634 AC: 43115 AN: 67972

Other (OTH) AF: 0.580 AC: 1226 AN: 2112

Alfa AF: 0.619 Hom.: 20979

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
PhyloP100		-0.053

Splicing

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

Other links and lift over

dbSNP: rs2855475; hg19: chr16-31147548;