16-85710232-ACGTCCAGGTGCTTGTCGTTC-A

Position:

• chr16-85710232-ACGTCCAGGTGCTTGTCGTTC-A

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2

The ENST00000284245.9(C16orf74):​c.84_103del​(p.Asn29AlafsTer27) variant causes a frameshift change. The variant allele was found at a frequency of 0.00208 in 1,503,882 control chromosomes in the GnomAD database, including 21 homozygotes. Variant has been reported in ClinVar as not provided (no stars).

• Frequency:
  • Genomes: 𝑓 0.0019 (3 hom., cov: 33)
  • Exomes 𝑓: 0.0021 (18 hom.)
• Consequence: C16orf74 ENST00000284245.9 frameshift
• Clinical Significance: not provided no classification provided O:1
• Conservation: PhyloP100: 5.17

Genes affected

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

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BS2: High Homozygotes in GnomAd4 at 3 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C16orf74	NM_206967.3	c.84_103del	p.Asn29AlafsTer27	frameshift_variant	3/4	ENST00000284245.9	NP_996850.1
C16orf74	NR_161452.1	n.315_334del		non_coding_transcript_exon_variant	4/5
C16orf74	NR_161454.1	n.251_270del		non_coding_transcript_exon_variant	3/4
C16orf74	NR_161453.1	n.218-2186_218-2167del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C16orf74	ENST00000284245.9	c.84_103del	p.Asn29AlafsTer27	frameshift_variant	3/4	1	NM_206967.3	ENSP00000284245	P1
	ENST00000655120.1	n.1042_1061del		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.00194 AC: 295 AN: 152204 Hom.: 3 Cov.: 33

Gnomad AFR AF: 0.000507

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000458

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000565

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00216

Gnomad OTH AF: 0.00239

GnomAD3 exomes AF: 0.00223 AC: 298 AN: 133570 Hom.: 3 AF XY: 0.00232 AC XY: 175 AN XY: 75484

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.000609

Gnomad ASJ exome AF: 0.0300

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.000123

Gnomad NFE exome AF: 0.00144

Gnomad OTH exome AF: 0.00386

GnomAD4 exome AF: 0.00210 AC: 2839 AN: 1351560 Hom.: 18 AF XY: 0.00210 AC XY: 1406 AN XY: 668096

Gnomad4 AFR exome AF: 0.000112

Gnomad4 AMR exome AF: 0.000520

Gnomad4 ASJ exome AF: 0.0315

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.000346

Gnomad4 NFE exome AF: 0.00176

Gnomad4 OTH exome AF: 0.00365

GnomAD4 genome AF: 0.00194 AC: 295 AN: 152322 Hom.: 3 Cov.: 33 AF XY: 0.00164 AC XY: 122 AN XY: 74492

Gnomad4 AFR AF: 0.000505

Gnomad4 AMR AF: 0.000457

Gnomad4 ASJ AF: 0.0314

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000565

Gnomad4 NFE AF: 0.00216

Gnomad4 OTH AF: 0.00237

Alfa AF: 0.00517 Hom.: 4

Bravo AF: 0.00192

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

Submissions by phenotype

not provided Other:1

not provided, no classification provided

phenotyping only

GenomeConnect, ClinGen

-

GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -

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: rs767753044; hg19: chr16-85743838;