16-85697343-C-T

Variant names:

• chr16-85697343-C-T
• rs402939
• ENST00000614011.2:n.766G>A

Variant summary

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

The ENST00000614011.2(ENSG00000275393):​n.766G>A 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 0.947 in 152,298 control chromosomes in the GnomAD database, including 68,764 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 0.95 (68764 hom., cov: 33)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000275393 ENST00000614011.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.752
• Publications: 0 publications found

Genes affected

ENSG00000275393 (HGNC:):

C16orf74 (HGNC:23362): (chromosome 16 open reading frame 74)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.993 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
ENSG00000275393	ENST00000614011.2	n.766G>A		non_coding_transcript_exon_variant	Exon 2 of 2	6
C16orf74	ENST00000602719.5	c.173-6566G>A		intron_variant	Intron 3 of 3	3		ENSP00000473398.1
C16orf74	ENST00000602758.1	n.86-6566G>A		intron_variant	Intron 1 of 1	2

Frequencies

GnomAD3 genomes AF: 0.947 AC: 144152 AN: 152180 Hom.: 68735 Cov.: 33

Gnomad AFR AF: 0.819

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.978

Gnomad ASJ AF: 1.00

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.989

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.999

Gnomad OTH AF: 0.957

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.947 AC: 144232 AN: 152298 Hom.: 68764 Cov.: 33 AF XY: 0.948 AC XY: 70595 AN XY: 74468

African (AFR) AF: 0.819 AC: 34004 AN: 41534

American (AMR) AF: 0.978 AC: 14966 AN: 15298

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 3472 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5184 AN: 5184

South Asian (SAS) AF: 0.989 AC: 4774 AN: 4828

European-Finnish (FIN) AF: 1.00 AC: 10622 AN: 10622

Middle Eastern (MID) AF: 0.983 AC: 289 AN: 294

European-Non Finnish (NFE) AF: 0.999 AC: 67982 AN: 68038

Other (OTH) AF: 0.958 AC: 2027 AN: 2116

Alfa AF: 0.952 Hom.: 55452

Bravo AF: 0.940

Asia WGS AF: 0.982 AC: 3414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.59
PhyloP100		-0.75
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs402939; hg19: chr16-85730949;