15-89477180-CC-GA

Variant names:

• chr15-89477180-CC-GA
• NM_016321.3:c.1138_1139delGGinsTC
• RHCG p.Gly380Ser

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_016321.3(RHCG):​c.1138_1139delGGinsTC​(p.Gly380Ser) variant causes a missense 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 MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: RHCG NM_016321.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.03
• Publications: 0 publications found

Genes affected

RHCG (HGNC:18140): (Rh family C glycoprotein) Enables ammonium transmembrane transporter activity; ankyrin binding activity; and identical protein binding activity. Involved in ammonium transmembrane transport; cellular ion homeostasis; and transepithelial ammonium transport. Located in apical plasma membrane and basolateral plasma membrane. Is integral component of plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016321.3. 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
	RHCG	NM_016321.3	MANE Select	c.1138_1139delGGinsTC	p.Gly380Ser	missense	N/A	NP_057405.1	Q9UBD6
	RHCG	NM_001321041.2		c.1138_1139delGGinsTC	p.Gly380Ser	missense	N/A	NP_001307970.1	Q9UBD6
	RHCG	NR_110261.2		n.1101_1102delGGinsTC		non_coding_transcript_exon	Exon 8 of 11

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	RHCG	ENST00000268122.9	TSL:1 MANE Select	c.1138_1139delGGinsTC	p.Gly380Ser	missense	N/A	ENSP00000268122.4	Q9UBD6
	RHCG	ENST00000560081.5	TSL:1	n.*66_*67delGGinsTC		non_coding_transcript_exon	Exon 8 of 11	ENSP00000453588.1	H0YMF8
	RHCG	ENST00000560081.5	TSL:1	n.*66_*67delGGinsTC		3_prime_UTR	Exon 8 of 11	ENSP00000453588.1	H0YMF8

Frequencies

GnomAD3 genomes Cov.: 32

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

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		1.0

Splicing

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: chr15-90020411;