rs910563

Variant names:

• chr6-87349167-G-A
• rs910563
• NM_001010868.3:c.243+261G>A

Variant summary

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

The NM_001010868.3(C6orf163):​c.243+261G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 151,918 control chromosomes in the GnomAD database, including 14,559 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 0.43 (14559 hom., cov: 31)
• Consequence: C6orf163 NM_001010868.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301
• Publications: 9 publications found

Genes affected

C6orf163 (HGNC:21403): (chromosome 6 open reading frame 163)

SMIM8 (HGNC:21401): (small integral membrane protein 8) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.479 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001010868.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C6orf163	NM_001010868.3	MANE Select	c.243+261G>A		intron	N/A	NP_001010868.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	C6orf163	ENST00000388923.5	TSL:5 MANE Select	c.243+261G>A		intron	N/A	ENSP00000373575.3
	SMIM8	ENST00000448282.6	TSL:1	n.135+12001G>A		intron	N/A	ENSP00000476881.1
	C6orf163	ENST00000608326.1	TSL:2	c.-40+261G>A		intron	N/A	ENSP00000477323.1

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65659 AN: 151800 Hom.: 14547 Cov.: 31

Gnomad AFR AF: 0.357

Gnomad AMI AF: 0.462

Gnomad AMR AF: 0.348

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.415

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.432 AC: 65702 AN: 151918 Hom.: 14559 Cov.: 31 AF XY: 0.432 AC XY: 32037 AN XY: 74236

African (AFR) AF: 0.357 AC: 14801 AN: 41408

American (AMR) AF: 0.348 AC: 5313 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1761 AN: 3466

East Asian (EAS) AF: 0.415 AC: 2145 AN: 5166

South Asian (SAS) AF: 0.423 AC: 2033 AN: 4808

European-Finnish (FIN) AF: 0.507 AC: 5349 AN: 10542

Middle Eastern (MID) AF: 0.421 AC: 123 AN: 292

European-Non Finnish (NFE) AF: 0.483 AC: 32822 AN: 67936

Other (OTH) AF: 0.442 AC: 934 AN: 2112

Alfa AF: 0.451 Hom.: 2340

Bravo AF: 0.416

Asia WGS AF: 0.364 AC: 1269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.33
PhyloP100		0.30
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs910563; hg19: chr6-88058885;