16-87126875-T-G

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

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
C16orf95	ENST00000562840.1	n.1305+11549A>C		intron_variant	Intron 4 of 4	2

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

Gnomad4 AFR AF: 0.790

Gnomad4 AMR AF: 0.657

Gnomad4 ASJ AF: 0.815

Gnomad4 EAS AF: 0.628

Gnomad4 SAS AF: 0.610

Gnomad4 FIN AF: 0.553

Gnomad4 NFE AF: 0.688

Gnomad4 OTH AF: 0.701

Alfa AF: 0.690 Hom.: 47281

Bravo AF: 0.718

Asia WGS AF: 0.590 AC: 2055 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2076962; hg19: chr16-87160481;