16-85710272-GGCTGCTGCT-GGCTGCT

Variant names:

• chr16-85710277-CTGC-C
• NM_206967.3:c.56_58delGCA

Variant summary

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

The NM_206967.3(C16orf74):​c.56_58delGCA​(p.Ser20del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 33)
• Consequence: C16orf74 NM_206967.3 conservative_inframe_deletion
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.83
• Publications: 0 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.56_58delGCA	p.Ser20del	conservative_inframe_deletion	Exon 3 of 4	NP_996850.1	Q96GX8-1
	C16orf74	NR_161452.1		n.287_289delGCA		non_coding_transcript_exon	Exon 4 of 5
	C16orf74	NR_161454.1		n.223_225delGCA		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.56_58delGCA	p.Ser20del	conservative_inframe_deletion	Exon 3 of 4	ENSP00000284245.3	Q96GX8-1
	C16orf74	ENST00000602583.5	TSL:1	c.20_22delGCA	p.Ser8del	conservative_inframe_deletion	Exon 1 of 2	ENSP00000473536.1	Q96GX8-2
	C16orf74	ENST00000602675.5	TSL:1	c.-86_-84delGCA		5_prime_UTR	Exon 3 of 4	ENSP00000473306.1	R4GMV5

Frequencies

GnomAD3 genomes Cov.: 33

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

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.8

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

hg19: chr16-85743883;