16-90029208-G-GGGCTGCCCCGCA

Variant names:

• chr16-90029208-G-GGGCTGCCCCGCA
• rs1555648296
• NM_001481.3:c.90+1487_90+1488insGCTGCCCCGCAG

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP6

The NM_001481.3(DRC4):​c.90+1487_90+1488insGCTGCCCCGCAG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Likely benign (no stars).

• Frequency: Genomes: not found (cov: 34)
• Consequence: DRC4 NM_001481.3 intron
• Clinical Significance: Likely benign no assertion criteria provided B:1
• Conservation: PhyloP100: -0.0640
• Publications: 0 publications found

Genes affected

DRC4 (HGNC:4166): (growth arrest specific 8) This gene includes 11 exons spanning 25 kb and maps to a region of chromosome 16 that is sometimes deleted in breast and prostrate cancer. The second intron contains an apparently intronless gene, C16orf3, that is transcribed in the opposite orientation. This gene is a putative tumor suppressor gene. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2013]

GAS8-AS1 (HGNC:1197): (GAS8 antisense RNA 1) This gene encodes a long non-coding RNA (lncRNA) that may function as a tumor suppressor. Mutations in this gene have been identified in human papillary thyroid carcinoma (PTC) patients that abrogate the ability of encoded lncRNA to inhibit cancer cell growth. [provided by RefSeq, May 2017]

ACMG classification

Our verdict: Likely_benign. The variant received -1 ACMG points.

• BP6: Variant 16-90029208-G-GGGCTGCCCCGCA is Benign according to our data. Variant chr16-90029208-G-GGGCTGCCCCGCA is described in ClinVar as Likely_benign. ClinVar VariationId is 212708.Status of the report is no_assertion_criteria_provided, 0 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001481.3. 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
	DRC4	NM_001481.3	MANE Select	c.90+1487_90+1488insGCTGCCCCGCAG		intron	N/A	NP_001472.1	O95995-1
	DRC4	NM_001286209.2		c.15+1487_15+1488insGCTGCCCCGCAG		intron	N/A	NP_001273138.1	O95995-2
	DRC4	NM_001286205.2		c.-283+1487_-283+1488insGCTGCCCCGCAG		intron	N/A	NP_001273134.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GAS8	ENST00000268699.9	TSL:1 MANE Select	c.90+1487_90+1488insGCTGCCCCGCAG		intron	N/A	ENSP00000268699.4	O95995-1
	GAS8	ENST00000566266.5	TSL:1	n.90+1487_90+1488insGCTGCCCCGCAG		intron	N/A	ENSP00000454343.1	H3BME0
	GAS8	ENST00000889287.1		c.90+1487_90+1488insGCTGCCCCGCAG		intron	N/A	ENSP00000559346.1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 34

ClinVar

ClinVar submissions

Significance: Likely benign

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
-	-	1	Autism (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.064

Splicing

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

Other links and lift over

dbSNP: rs1555648296; hg19: chr16-90095616;