16-31136227-G-A

Position:

• chr16-31136227-G-A

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;