6-87347412-A-G

Position:

• chr6-87347412-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001010868.3(C6orf163):​c.149-1400A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.59 in 983,500 control chromosomes in the GnomAD database, including 171,633 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 0.59 (26756 hom., cov: 33)
  • Exomes 𝑓: 0.59 (144877 hom.)
• Consequence: C6orf163 NM_001010868.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56

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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
C6orf163	NM_001010868.3	c.149-1400A>G		intron_variant		ENST00000388923.5	NP_001010868.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
C6orf163	ENST00000388923.5	c.149-1400A>G		intron_variant		5	NM_001010868.3	ENSP00000373575.3
SMIM8	ENST00000448282.6	n.135+10246A>G		intron_variant		1		ENSP00000476881.1
SMIM8	ENST00000369572.3	n.13+24780A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.589 AC: 89546 AN: 151960 Hom.: 26724 Cov.: 33

Gnomad AFR AF: 0.631

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.542

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.578

GnomAD4 exome AF: 0.590 AC: 490233 AN: 831422 Hom.: 144877 Cov.: 26 AF XY: 0.589 AC XY: 226291 AN XY: 384054

Gnomad4 AFR exome AF: 0.623

Gnomad4 AMR exome AF: 0.397

Gnomad4 ASJ exome AF: 0.585

Gnomad4 EAS exome AF: 0.535

Gnomad4 SAS exome AF: 0.525

Gnomad4 FIN exome AF: 0.638

Gnomad4 NFE exome AF: 0.591

Gnomad4 OTH exome AF: 0.578

GnomAD4 genome AF: 0.589 AC: 89635 AN: 152078 Hom.: 26756 Cov.: 33 AF XY: 0.586 AC XY: 43606 AN XY: 74350

Gnomad4 AFR AF: 0.632

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.543

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.625

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.580

Alfa AF: 0.587 Hom.: 44142

Bravo AF: 0.577

Asia WGS AF: 0.553 AC: 1926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.39
DANN	Benign	0.41

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: rs381798; hg19: chr6-88057130;