6-87347412-A-G

Variant names:

• chr6-87347412-A-G
• rs381798
• NM_001010868.3:c.149-1400A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 10 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=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.625 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.149-1400A>G		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.149-1400A>G		intron	N/A	ENSP00000373575.3
	SMIM8	ENST00000448282.6	TSL:1	n.135+10246A>G		intron	N/A	ENSP00000476881.1
	SMIM8	ENST00000369572.3	TSL:5	n.13+24780A>G		intron	N/A

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

African (AFR) AF: 0.623 AC: 9805 AN: 15728

American (AMR) AF: 0.397 AC: 391 AN: 984

Ashkenazi Jewish (ASJ) AF: 0.585 AC: 3011 AN: 5144

East Asian (EAS) AF: 0.535 AC: 1937 AN: 3622

South Asian (SAS) AF: 0.525 AC: 8618 AN: 16430

European-Finnish (FIN) AF: 0.638 AC: 176 AN: 276

Middle Eastern (MID) AF: 0.564 AC: 913 AN: 1620

European-Non Finnish (NFE) AF: 0.591 AC: 449632 AN: 760388

Other (OTH) AF: 0.578 AC: 15750 AN: 27230

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

African (AFR) AF: 0.632 AC: 26203 AN: 41472

American (AMR) AF: 0.456 AC: 6964 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.573 AC: 1987 AN: 3470

East Asian (EAS) AF: 0.543 AC: 2809 AN: 5176

South Asian (SAS) AF: 0.543 AC: 2618 AN: 4822

European-Finnish (FIN) AF: 0.625 AC: 6608 AN: 10574

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.597 AC: 40599 AN: 67962

Other (OTH) AF: 0.580 AC: 1227 AN: 2114

Alfa AF: 0.588 Hom.: 73934

Bravo AF: 0.577

Asia WGS AF: 0.553 AC: 1926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.39
DANN	Benign	0.41
PhyloP100		-1.6
PromoterAI		0.0042	Neutral
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: rs381798; hg19: chr6-88057130;