NM_206967.3:c.55_63dupAGCAGCAGC

Variant names:

• chr16-85710272-G-GGCTGCTGCT
• rs751825593
• NM_206967.3:c.55_63dupAGCAGCAGC

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP3

The NM_206967.3(C16orf74):​c.55_63dupAGCAGCAGC​(p.Ser19_Ser21dup) variant causes a conservative inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000221 in 1,357,814 control chromosomes in the GnomAD database, with no homozygous occurrence. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000022 (0 hom.)
• Consequence: C16orf74 NM_206967.3 conservative_inframe_insertion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.57
• Publications: 1 publications found

Genes affected

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

ENSG00000287125 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP3: Nonframeshift variant in repetitive region in NM_206967.3

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_206967.3. 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
	C16orf74	NM_206967.3	MANE Select	c.55_63dupAGCAGCAGC	p.Ser19_Ser21dup	conservative_inframe_insertion	Exon 3 of 4	NP_996850.1	Q96GX8-1
	C16orf74	NR_161452.1		n.286_294dupAGCAGCAGC		non_coding_transcript_exon	Exon 4 of 5
	C16orf74	NR_161454.1		n.222_230dupAGCAGCAGC		non_coding_transcript_exon	Exon 3 of 4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C16orf74	ENST00000284245.9	TSL:1 MANE Select	c.55_63dupAGCAGCAGC	p.Ser19_Ser21dup	conservative_inframe_insertion	Exon 3 of 4	ENSP00000284245.3	Q96GX8-1
	C16orf74	ENST00000602583.5	TSL:1	c.19_27dupAGCAGCAGC	p.Ser7_Ser9dup	conservative_inframe_insertion	Exon 1 of 2	ENSP00000473536.1	Q96GX8-2
	C16orf74	ENST00000602675.5	TSL:1	c.-87_-79dupAGCAGCAGC		5_prime_UTR	Exon 3 of 4	ENSP00000473306.1	R4GMV5

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000221 AC: 3 AN: 1357814 Hom.: 0 Cov.: 33 AF XY: 0.00000298 AC XY: 2 AN XY: 671722

African (AFR) AF: 0.00 AC: 0 AN: 27640

American (AMR) AF: 0.00 AC: 0 AN: 26274

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 23612

East Asian (EAS) AF: 0.0000621 AC: 2 AN: 32196

South Asian (SAS) AF: 0.00 AC: 0 AN: 71336

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 44548

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5532

European-Non Finnish (NFE) AF: 9.34e-7 AC: 1 AN: 1070346

Other (OTH) AF: 0.00 AC: 0 AN: 56330

GnomAD4 genome Cov.: 33

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.6

Splicing

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

Other links and lift over

dbSNP: rs751825593; hg19: chr16-85743878;