chr16-49130730-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000287469 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000287469	ENST00000655430.1	n.78-16564A>G		intron_variant	Intron 1 of 2
ENSG00000287469	ENST00000659681.1	n.70-16564A>G		intron_variant	Intron 1 of 2

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

Gnomad4 AFR AF: 0.278

Gnomad4 AMR AF: 0.438

Gnomad4 ASJ AF: 0.504

Gnomad4 EAS AF: 0.493

Gnomad4 SAS AF: 0.288

Gnomad4 FIN AF: 0.397

Gnomad4 NFE AF: 0.449

Gnomad4 OTH AF: 0.419

Alfa AF: 0.431 Hom.: 8254

Bravo AF: 0.405

Asia WGS AF: 0.327 AC: 1136 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1510986; hg19: chr16-49164641;