rs910563

Positions:

• chr6-87349167-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C6orf163	NM_001010868.3	c.243+261G>A		intron_variant		ENST00000388923.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C6orf163	ENST00000388923.5	c.243+261G>A		intron_variant		5	NM_001010868.3	P1
SMIM8	ENST00000448282.6	c.135+12001G>A		intron_variant, NMD_transcript_variant		1
C6orf163	ENST00000608326.1	c.-40+261G>A		intron_variant		2
SMIM8	ENST00000369572.3	n.14-26295G>A		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.357

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.415

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.507

Gnomad4 NFE AF: 0.483

Gnomad4 OTH AF: 0.442

Alfa AF: 0.454 Hom.: 2278

Bravo AF: 0.416

Asia WGS AF: 0.364 AC: 1269 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.1
DANN	Benign	0.33

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: rs910563; hg19: chr6-88058885;