rs242264

chr6-87351020-T-C

Variant summary

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

The NM_001010868.3(C6orf163):c.351+519T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.592 in 151,944 control chromosomes in the GnomAD database, including 26,985 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 (26985 hom., cov: 31)
• Consequence: C6orf163 NM_001010868.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
C6orf163	NM_001010868.3	c.351+519T>C		intron_variant		ENST00000388923.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
C6orf163	ENST00000388923.5	c.351+519T>C		intron_variant		5	NM_001010868.3	P1
SMIM8	ENST00000448282.6	c.135+13854T>C		intron_variant, NMD_transcript_variant		1
C6orf163	ENST00000608326.1	c.-40+2114T>C		intron_variant		2
SMIM8	ENST00000369572.3	n.14-24442T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.592 AC: 89855 AN: 151826 Hom.: 26955 Cov.: 31

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.513

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.541

Gnomad SAS AF: 0.515

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.592 AC: 89942 AN: 151944 Hom.: 26985 Cov.: 31 AF XY: 0.589 AC XY: 43704 AN XY: 74260

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.457

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.541

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.624

Gnomad4 NFE AF: 0.598

Gnomad4 OTH AF: 0.582

Alfa AF: 0.585 Hom.: 12687

Bravo AF: 0.581

Asia WGS AF: 0.542 AC: 1890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	1.0
Dann	Benign	0.70

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: rs242264; hg19: chr6-88060738;