6-31660956-C-T

Variant names:

• chr6-31660956-C-T
• rs805262
• NM_021184.4:c.-1009G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_021184.4(C6orf47):​c.-1009G>A variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.363 in 152,100 control chromosomes in the GnomAD database, including 12,068 homozygotes. 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: 𝑓 0.36 (12068 hom., cov: 32)
• Consequence: C6orf47 NM_021184.4 upstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 46 publications found

Genes affected

C6orf47 (HGNC:19076): (chromosome 6 open reading frame 47)

C6orf47-AS1 (HGNC:39767): (C6orf47 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021184.4. 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
	C6orf47	NM_021184.4	MANE Select	c.-1009G>A		upstream_gene	N/A	NP_067007.3	A0A1U9X7F2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C6orf47	ENST00000375911.2	TSL:6 MANE Select	c.-1009G>A		upstream_gene	N/A	ENSP00000365076.1	O95873
	C6orf47-AS1	ENST00000422049.1	TSL:2	n.*235C>T		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.363 AC: 55219 AN: 151982 Hom.: 12065 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.587

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.439

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.472

Gnomad OTH AF: 0.370

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

GnomAD4 genome AF: 0.363 AC: 55227 AN: 152100 Hom.: 12068 Cov.: 32 AF XY: 0.362 AC XY: 26943 AN XY: 74342

African (AFR) AF: 0.114 AC: 4729 AN: 41528

American (AMR) AF: 0.374 AC: 5723 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.587 AC: 2036 AN: 3470

East Asian (EAS) AF: 0.574 AC: 2962 AN: 5162

South Asian (SAS) AF: 0.439 AC: 2114 AN: 4818

European-Finnish (FIN) AF: 0.394 AC: 4170 AN: 10572

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.472 AC: 32050 AN: 67954

Other (OTH) AF: 0.370 AC: 780 AN: 2108

Alfa AF: 0.453 Hom.: 70492

Bravo AF: 0.350

Asia WGS AF: 0.435 AC: 1515 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	5.9
DANN	Benign	0.79
PhyloP100		-0.28
PromoterAI		-0.027	Neutral

Splicing

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

Other links and lift over

dbSNP: rs805262; hg19: chr6-31628733;