rs200271005

Variant names:

• chr6-42105293-G-A
• rs200271005
• NM_001164446.3:c.2619C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-42105293-G-A
• chr6-42105293-G-C
• chr6-42105293-G-T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_001164446.3(C6orf132):​c.2619C>T​(p.His873His) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: C6orf132 NM_001164446.3 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.204

Genes affected

C6orf132 (HGNC:21288): (chromosome 6 open reading frame 132)

ACMG classification

Verdict is Likely_benign. Variant got -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BP7: Synonymous conserved (PhyloP=0.204 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
C6orf132	NM_001164446.3	c.2619C>T	p.His873His	synonymous_variant	Exon 4 of 5	ENST00000341865.9	NP_001157918.1
C6orf132	XM_047419258.1	c.2064C>T	p.His688His	synonymous_variant	Exon 3 of 4		XP_047275214.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
C6orf132	ENST00000341865.9	c.2619C>T	p.His873His	synonymous_variant	Exon 4 of 5	5	NM_001164446.3	ENSP00000341368.4
C6orf132	ENST00000696229.1	n.*3231C>T		non_coding_transcript_exon_variant	Exon 5 of 6			ENSP00000512495.1
C6orf132	ENST00000696229.1	n.*3231C>T		3_prime_UTR_variant	Exon 5 of 6			ENSP00000512495.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD3 exomes AF: 0.00000705 AC: 1 AN: 141892 Hom.: 0 AF XY: 0.0000132 AC XY: 1 AN XY: 75858

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.000185

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 50

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.0
DANN	Benign	0.51

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs200271005; hg19: chr6-42073031;