chr16-51426960-A-G

Variant names:

• chr16-51426960-A-G
• rs2063099
• ENST00000642667.1:n.393-10397A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000642667.1(ENSG00000285367):​n.393-10397A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.484 in 152,032 control chromosomes in the GnomAD database, including 19,348 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 0.48 (19348 hom., cov: 32)
• Consequence: ENSG00000285367 ENST00000642667.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.92
• Publications: 8 publications found

Genes affected

ENSG00000285367 (HGNC:58539):

ENSG00000260850 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.922 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642667.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285367	ENST00000642667.1		n.393-10397A>G		intron	N/A
	ENSG00000260850	ENST00000643262.1		n.399+68142T>C		intron	N/A
	ENSG00000260850	ENST00000646267.1		n.390-22332T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.484 AC: 73579 AN: 151914 Hom.: 19312 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.588

Gnomad ASJ AF: 0.489

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.532

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.484 AC: 73654 AN: 152032 Hom.: 19348 Cov.: 32 AF XY: 0.493 AC XY: 36607 AN XY: 74300

African (AFR) AF: 0.327 AC: 13548 AN: 41452

American (AMR) AF: 0.589 AC: 8992 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.489 AC: 1696 AN: 3470

East Asian (EAS) AF: 0.944 AC: 4881 AN: 5168

South Asian (SAS) AF: 0.709 AC: 3413 AN: 4816

European-Finnish (FIN) AF: 0.532 AC: 5621 AN: 10574

Middle Eastern (MID) AF: 0.493 AC: 145 AN: 294

European-Non Finnish (NFE) AF: 0.500 AC: 33957 AN: 67956

Other (OTH) AF: 0.496 AC: 1049 AN: 2116

Alfa AF: 0.486 Hom.: 37740

Bravo AF: 0.483

Asia WGS AF: 0.769 AC: 2673 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.041
DANN	Benign	0.45
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs2063099; hg19: chr16-51460871;