16-2868291-A-G

Variant names:

• chr16-2868291-A-G
• rs17660212
• ENST00000834243.1:n.243T>C

Variant summary

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

The ENST00000834243.1(ENSG00000263280):​n.243T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,214 control chromosomes in the GnomAD database, including 6,925 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 0.26 (6925 hom., cov: 34)
• Consequence: ENSG00000263280 ENST00000834243.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• Publications: 11 publications found

Genes affected

ENSG00000263280 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000834243.1. 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
	LOC101929566	NR_188573.1		n.-87T>C		upstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000263280	ENST00000834243.1		n.243T>C		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000263280	ENST00000834249.1		n.146T>C		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000263280	ENST00000575693.3	TSL:3	n.-27T>C		upstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40327 AN: 152096 Hom.: 6927 Cov.: 34

Gnomad AFR AF: 0.0805

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.0988

Gnomad FIN AF: 0.297

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.392

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.265 AC: 40313 AN: 152214 Hom.: 6925 Cov.: 34 AF XY: 0.256 AC XY: 19014 AN XY: 74390

African (AFR) AF: 0.0803 AC: 3336 AN: 41570

American (AMR) AF: 0.273 AC: 4183 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1466 AN: 3466

East Asian (EAS) AF: 0.00270 AC: 14 AN: 5180

South Asian (SAS) AF: 0.0998 AC: 481 AN: 4822

European-Finnish (FIN) AF: 0.297 AC: 3147 AN: 10590

Middle Eastern (MID) AF: 0.378 AC: 111 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26608 AN: 67968

Other (OTH) AF: 0.334 AC: 706 AN: 2116

Alfa AF: 0.350 Hom.: 5254

Bravo AF: 0.258

Asia WGS AF: 0.0570 AC: 199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.42
DANN	Benign	0.25
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs17660212; hg19: chr16-2918292;