ENST00000562840.1:n.1305+11549A>C

Variant names:

• chr16-87126875-T-G
• rs2076962
• ENST00000562840.1:n.1305+11549A>C

Variant summary

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

The ENST00000562840.1(C16orf95):​n.1305+11549A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.702 in 152,140 control chromosomes in the GnomAD database, including 38,102 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 0.70 (38102 hom., cov: 33)
• Consequence: C16orf95 ENST00000562840.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.82
• Publications: 7 publications found

Genes affected

C16orf95 (HGNC:40033): (chromosome 16 open reading frame 95)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.783 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000562840.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C16orf95	ENST00000562840.1	TSL:2	n.1305+11549A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.702 AC: 106782 AN: 152022 Hom.: 38070 Cov.: 33

Gnomad AFR AF: 0.791

Gnomad AMI AF: 0.753

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.815

Gnomad EAS AF: 0.628

Gnomad SAS AF: 0.610

Gnomad FIN AF: 0.553

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.688

Gnomad OTH AF: 0.704

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

GnomAD4 genome AF: 0.702 AC: 106866 AN: 152140 Hom.: 38102 Cov.: 33 AF XY: 0.694 AC XY: 51569 AN XY: 74348

African (AFR) AF: 0.790 AC: 32813 AN: 41512

American (AMR) AF: 0.657 AC: 10050 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.815 AC: 2828 AN: 3472

East Asian (EAS) AF: 0.628 AC: 3243 AN: 5166

South Asian (SAS) AF: 0.610 AC: 2942 AN: 4820

European-Finnish (FIN) AF: 0.553 AC: 5847 AN: 10566

Middle Eastern (MID) AF: 0.721 AC: 212 AN: 294

European-Non Finnish (NFE) AF: 0.688 AC: 46764 AN: 68000

Other (OTH) AF: 0.701 AC: 1482 AN: 2114

Alfa AF: 0.695 Hom.: 60906

Bravo AF: 0.718

Asia WGS AF: 0.590 AC: 2055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.30
DANN	Benign	0.49
PhyloP100		-1.8

Splicing

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

Other links and lift over

dbSNP: rs2076962; hg19: chr16-87160481;