16-49130730-T-C

Variant names:

• chr16-49130730-T-C
• rs1510986
• ENST00000655430.1:n.78-16564A>G

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000655430.1(ENSG00000287469):​n.78-16564A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.396 in 151,460 control chromosomes in the GnomAD database, including 12,469 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 0.40 (12469 hom., cov: 31)
• Consequence: ENSG00000287469 ENST00000655430.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.11
• Publications: 3 publications found

Genes affected

ENSG00000287469 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.2).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.477 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000655430.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000287469	ENST00000655430.1		n.78-16564A>G		intron	N/A
	ENSG00000287469	ENST00000659681.1		n.70-16564A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.396 AC: 59928 AN: 151346 Hom.: 12466 Cov.: 31

Gnomad AFR AF: 0.278

Gnomad AMI AF: 0.561

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.504

Gnomad EAS AF: 0.494

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.468

Gnomad NFE AF: 0.449

Gnomad OTH AF: 0.424

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

GnomAD4 genome AF: 0.396 AC: 59934 AN: 151460 Hom.: 12469 Cov.: 31 AF XY: 0.392 AC XY: 28990 AN XY: 73976

African (AFR) AF: 0.278 AC: 11443 AN: 41230

American (AMR) AF: 0.438 AC: 6665 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.504 AC: 1748 AN: 3466

East Asian (EAS) AF: 0.493 AC: 2530 AN: 5134

South Asian (SAS) AF: 0.288 AC: 1382 AN: 4802

European-Finnish (FIN) AF: 0.397 AC: 4160 AN: 10472

Middle Eastern (MID) AF: 0.490 AC: 144 AN: 294

European-Non Finnish (NFE) AF: 0.449 AC: 30481 AN: 67840

Other (OTH) AF: 0.419 AC: 875 AN: 2088

Alfa AF: 0.431 Hom.: 9101

Bravo AF: 0.405

Asia WGS AF: 0.327 AC: 1136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.20
CADD	Benign	14
DANN	Benign	0.70
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs1510986; hg19: chr16-49164641;