16-14267460-C-G

Variant names:

• chr16-14267460-C-G
• rs30121
• ENST00000814264.1:n.128-11357G>C

Variant summary

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

The ENST00000814264.1(ENSG00000305939):​n.128-11357G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.11 in 152,212 control chromosomes in the GnomAD database, including 1,237 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 0.11 (1237 hom., cov: 32)
• Consequence: ENSG00000305939 ENST00000814264.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.198
• Publications: 2 publications found

Genes affected

ENSG00000305939 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.288 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000814264.1. 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
	ENSG00000305939	ENST00000814264.1		n.128-11357G>C		intron	N/A
	ENSG00000305939	ENST00000814265.1		n.126-11357G>C		intron	N/A
	ENSG00000305939	ENST00000814266.1		n.75-11353G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.110 AC: 16697 AN: 152094 Hom.: 1227 Cov.: 32

Gnomad AFR AF: 0.154

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.301

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.0520

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.0665

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.110 AC: 16754 AN: 152212 Hom.: 1237 Cov.: 32 AF XY: 0.113 AC XY: 8442 AN XY: 74418

African (AFR) AF: 0.155 AC: 6429 AN: 41512

American (AMR) AF: 0.117 AC: 1784 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 439 AN: 3468

East Asian (EAS) AF: 0.301 AC: 1556 AN: 5174

South Asian (SAS) AF: 0.219 AC: 1055 AN: 4828

European-Finnish (FIN) AF: 0.0520 AC: 552 AN: 10608

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.0665 AC: 4521 AN: 68012

Other (OTH) AF: 0.126 AC: 267 AN: 2112

Alfa AF: 0.0233 Hom.: 10

Bravo AF: 0.115

Asia WGS AF: 0.245 AC: 852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.1
DANN	Benign	0.67
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs30121; hg19: chr16-14361317;