16-49076955-G-C

Variant names:

• chr16-49076955-G-C
• rs1009303
• ENST00000655430.1:n.269-252C>G

Variant summary

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

The ENST00000655430.1(ENSG00000287469):​n.269-252C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.813 in 152,188 control chromosomes in the GnomAD database, including 50,809 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 0.81 (50809 hom., cov: 32)
• Consequence: ENSG00000287469 ENST00000655430.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.921
• Publications: 1 publications found

Genes affected

ENSG00000287469 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.971 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

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
	ENSG00000287469	ENST00000655430.1		n.269-252C>G		intron	N/A
	ENSG00000287469	ENST00000659681.1		n.261-252C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.813 AC: 123642 AN: 152070 Hom.: 50756 Cov.: 32

Gnomad AFR AF: 0.893

Gnomad AMI AF: 0.724

Gnomad AMR AF: 0.858

Gnomad ASJ AF: 0.789

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.882

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.816

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

GnomAD4 genome AF: 0.813 AC: 123754 AN: 152188 Hom.: 50809 Cov.: 32 AF XY: 0.815 AC XY: 60636 AN XY: 74404

African (AFR) AF: 0.893 AC: 37089 AN: 41524

American (AMR) AF: 0.858 AC: 13121 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.789 AC: 2741 AN: 3472

East Asian (EAS) AF: 0.994 AC: 5139 AN: 5172

South Asian (SAS) AF: 0.881 AC: 4248 AN: 4820

European-Finnish (FIN) AF: 0.706 AC: 7471 AN: 10588

Middle Eastern (MID) AF: 0.864 AC: 254 AN: 294

European-Non Finnish (NFE) AF: 0.754 AC: 51300 AN: 68002

Other (OTH) AF: 0.819 AC: 1732 AN: 2116

Alfa AF: 0.775 Hom.: 5699

Bravo AF: 0.830

Asia WGS AF: 0.936 AC: 3254 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.36
DANN	Benign	0.45
PhyloP100		-0.92

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1009303;

hg19: chr16-49110866;