rs2858942

Variant names:

• chr16-175654-A-C
• rs2858942
• ENST00000723842.1:n.27A>C

Variant summary

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

The ENST00000723842.1(ENSG00000294481):​n.27A>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 0.752 in 147,994 control chromosomes in the GnomAD database, including 43,348 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 0.75 (43348 hom., cov: 30)
• Consequence: ENSG00000294481 ENST00000723842.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• Publications: 32 publications found

Genes affected

ENSG00000294481 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.921 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
ENSG00000294481	ENST00000723842.1	n.27A>C		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.751 AC: 111126 AN: 147876 Hom.: 43287 Cov.: 30

Gnomad AFR AF: 0.929

Gnomad AMI AF: 0.782

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.701

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.753

Gnomad NFE AF: 0.700

Gnomad OTH AF: 0.711

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

GnomAD4 genome AF: 0.752 AC: 111249 AN: 147994 Hom.: 43348 Cov.: 30 AF XY: 0.746 AC XY: 53966 AN XY: 72344

African (AFR) AF: 0.929 AC: 35337 AN: 38032

American (AMR) AF: 0.703 AC: 10586 AN: 15056

Ashkenazi Jewish (ASJ) AF: 0.727 AC: 2516 AN: 3460

East Asian (EAS) AF: 0.514 AC: 2622 AN: 5106

South Asian (SAS) AF: 0.702 AC: 3252 AN: 4630

European-Finnish (FIN) AF: 0.661 AC: 6971 AN: 10554

Middle Eastern (MID) AF: 0.759 AC: 223 AN: 294

European-Non Finnish (NFE) AF: 0.700 AC: 47539 AN: 67868

Other (OTH) AF: 0.715 AC: 1491 AN: 2084

Alfa AF: 0.727 Hom.: 69110

Bravo AF: 0.767

Asia WGS AF: 0.663 AC: 2176 AN: 3286

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	1.0
DANN	Benign	0.42
PhyloP100		-1.9

Splicing

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

Other links and lift over

dbSNP: rs2858942; hg19: chr16-225653;