16-87255411-T-G

Variant names:

• chr16-87255411-T-G
• rs3748391
• ENST00000562840.1:n.110+47242A>C

Variant summary

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

The ENST00000562840.1(C16orf95):​n.110+47242A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.451 in 151,812 control chromosomes in the GnomAD database, including 16,476 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 0.45 (16476 hom., cov: 31)
• Consequence: C16orf95 ENST00000562840.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.972
• Publications: 11 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.567 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C16orf95	ENST00000562840.1	TSL:2	n.110+47242A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.451 AC: 68406 AN: 151694 Hom.: 16443 Cov.: 31

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.423

Gnomad EAS AF: 0.105

Gnomad SAS AF: 0.135

Gnomad FIN AF: 0.325

Gnomad MID AF: 0.433

Gnomad NFE AF: 0.466

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.451 AC: 68490 AN: 151812 Hom.: 16476 Cov.: 31 AF XY: 0.435 AC XY: 32295 AN XY: 74208

African (AFR) AF: 0.573 AC: 23705 AN: 41386

American (AMR) AF: 0.380 AC: 5785 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.423 AC: 1468 AN: 3468

East Asian (EAS) AF: 0.105 AC: 540 AN: 5148

South Asian (SAS) AF: 0.136 AC: 656 AN: 4806

European-Finnish (FIN) AF: 0.325 AC: 3431 AN: 10558

Middle Eastern (MID) AF: 0.441 AC: 128 AN: 290

European-Non Finnish (NFE) AF: 0.465 AC: 31609 AN: 67910

Other (OTH) AF: 0.437 AC: 919 AN: 2104

Alfa AF: 0.451 Hom.: 65235

Bravo AF: 0.461

Asia WGS AF: 0.166 AC: 581 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	0.61
DANN	Benign	0.51
PhyloP100		-0.97

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs3748391;

hg19: chr16-87289017;