chr16-85710272-GGCTGCT-G

Position:

• chr16-85710272-GGCTGCT-G

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP3 BP6_Moderate BS2

The ENST00000284245.9(C16orf74):​c.58_63del​(p.Ser20_Ser21del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00692 in 1,509,930 control chromosomes in the GnomAD database, including 46 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0048 (2 hom., cov: 33)
  • Exomes 𝑓: 0.0071 (44 hom.)
• Consequence: C16orf74 ENST00000284245.9 inframe_deletion
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 3.57

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -7 ACMG points.

• BP3: Nonframeshift variant in repetitive region in ENST00000284245.9
• BP6: Variant 16-85710272-GGCTGCT-G is Benign according to our data. Variant chr16-85710272-GGCTGCT-G is described in ClinVar as [Likely_benign]. Clinvar id is 2646943.Status of the report is criteria_provided_single_submitter, 1 stars.
• BS2: High Homozygotes in GnomAd4 at 2 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C16orf74	NM_206967.3	c.58_63del	p.Ser20_Ser21del	inframe_deletion	3/4	ENST00000284245.9	NP_996850.1
C16orf74	NR_161452.1	n.289_294del		non_coding_transcript_exon_variant	4/5
C16orf74	NR_161454.1	n.225_230del		non_coding_transcript_exon_variant	3/4
C16orf74	NR_161453.1	n.218-2212_218-2207del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C16orf74	ENST00000284245.9	c.58_63del	p.Ser20_Ser21del	inframe_deletion	3/4	1	NM_206967.3	ENSP00000284245	P1
	ENST00000655120.1	n.1095_1100del		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.00485 AC: 738 AN: 152106 Hom.: 2 Cov.: 33

Gnomad AFR AF: 0.00179

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00884

Gnomad ASJ AF: 0.00288

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00579

Gnomad FIN AF: 0.000566

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00687

Gnomad OTH AF: 0.00862

GnomAD3 exomes AF: 0.00435 AC: 483 AN: 111014 Hom.: 2 AF XY: 0.00443 AC XY: 279 AN XY: 63010

Gnomad AFR exome AF: 0.000882

Gnomad AMR exome AF: 0.00290

Gnomad ASJ exome AF: 0.00256

Gnomad EAS exome AF: 0.000188

Gnomad SAS exome AF: 0.00481

Gnomad FIN exome AF: 0.000263

Gnomad NFE exome AF: 0.00636

Gnomad OTH exome AF: 0.00385

GnomAD4 exome AF: 0.00715 AC: 9707 AN: 1357706 Hom.: 44 AF XY: 0.00721 AC XY: 4841 AN XY: 671660

Gnomad4 AFR exome AF: 0.00127

Gnomad4 AMR exome AF: 0.00415

Gnomad4 ASJ exome AF: 0.00305

Gnomad4 EAS exome AF: 0.0000932

Gnomad4 SAS exome AF: 0.00498

Gnomad4 FIN exome AF: 0.000898

Gnomad4 NFE exome AF: 0.00812

Gnomad4 OTH exome AF: 0.00632

GnomAD4 genome AF: 0.00484 AC: 737 AN: 152224 Hom.: 2 Cov.: 33 AF XY: 0.00450 AC XY: 335 AN XY: 74412

Gnomad4 AFR AF: 0.00178

Gnomad4 AMR AF: 0.00883

Gnomad4 ASJ AF: 0.00288

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00580

Gnomad4 FIN AF: 0.000566

Gnomad4 NFE AF: 0.00686

Gnomad4 OTH AF: 0.00853

Bravo AF: 0.00591

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2023

C16orf74: BS2; ENSG00000287125: BS2 -

Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs751825593; hg19: chr16-85743878;