16-87104018-T-G

Variant names:

• chr16-87104018-T-G
• rs7205422
• ENST00000562840.1:n.1306-20112A>C

Variant summary

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

The ENST00000562840.1(C16orf95):​n.1306-20112A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.159 in 152,064 control chromosomes in the GnomAD database, including 2,221 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 0.16 (2221 hom., cov: 31)
• Consequence: C16orf95 ENST00000562840.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302
• Publications: 1 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 (NFE) allele frequency at 95% confidence interval = 0.197 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.1306-20112A>C		intron_variant	Intron 4 of 4	2

Frequencies

GnomAD3 genomes AF: 0.160 AC: 24237 AN: 151946 Hom.: 2218 Cov.: 31

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.127

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.0309

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.221

Gnomad MID AF: 0.184

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.159 AC: 24241 AN: 152064 Hom.: 2221 Cov.: 31 AF XY: 0.158 AC XY: 11704 AN XY: 74308

African (AFR) AF: 0.103 AC: 4275 AN: 41512

American (AMR) AF: 0.126 AC: 1927 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 689 AN: 3470

East Asian (EAS) AF: 0.0307 AC: 159 AN: 5174

South Asian (SAS) AF: 0.164 AC: 786 AN: 4806

European-Finnish (FIN) AF: 0.221 AC: 2332 AN: 10558

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.199 AC: 13557 AN: 67960

Other (OTH) AF: 0.164 AC: 345 AN: 2104

Alfa AF: 0.182 Hom.: 330

Bravo AF: 0.147

Asia WGS AF: 0.0790 AC: 273 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	1.0
DANN	Benign	0.47
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs7205422; hg19: chr16-87137624;