1-151147269-G-C

Variant names:

• chr1-151147269-G-C
• rs3811402
• ENST00000866869.1:c.-930-15C>G

Variant summary

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

The ENST00000866869.1(SEMA6C):​c.-930-15C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0656 in 152,284 control chromosomes in the GnomAD database, including 451 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 0.066 (451 hom., cov: 32)
• Consequence: SEMA6C ENST00000866869.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0160
• Publications: 4 publications found

Genes affected

SEMA6C (HGNC:10740): (semaphorin 6C) This gene encodes a member of the semaphorin family. Semaphorins represent important molecular signals controlling multiple aspects of the cellular response that follows CNS injury, and thus may play an important role in neural regeneration. [provided by RefSeq, May 2010]

ENSG00000289288 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0958 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000866869.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SEMA6C	ENST00000866869.1		c.-930-15C>G		intron	N/A	ENSP00000536928.1
	SEMA6C	ENST00000866870.1		c.-584-15C>G		intron	N/A	ENSP00000536929.1
	SEMA6C	ENST00000866871.1		c.-253+397C>G		intron	N/A	ENSP00000536930.1

Frequencies

GnomAD3 genomes AF: 0.0657 AC: 9990 AN: 152166 Hom.: 450 Cov.: 32

Gnomad AFR AF: 0.0145

Gnomad AMI AF: 0.0746

Gnomad AMR AF: 0.100

Gnomad ASJ AF: 0.0455

Gnomad EAS AF: 0.0585

Gnomad SAS AF: 0.0828

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0788

Gnomad OTH AF: 0.0693

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

GnomAD4 genome AF: 0.0656 AC: 9990 AN: 152284 Hom.: 451 Cov.: 32 AF XY: 0.0700 AC XY: 5211 AN XY: 74454

African (AFR) AF: 0.0144 AC: 598 AN: 41566

American (AMR) AF: 0.0999 AC: 1528 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0455 AC: 158 AN: 3470

East Asian (EAS) AF: 0.0586 AC: 304 AN: 5184

South Asian (SAS) AF: 0.0831 AC: 401 AN: 4828

European-Finnish (FIN) AF: 0.134 AC: 1421 AN: 10602

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0788 AC: 5360 AN: 68022

Other (OTH) AF: 0.0691 AC: 146 AN: 2114

Alfa AF: 0.0250 Hom.: 20

Bravo AF: 0.0593

Asia WGS AF: 0.0690 AC: 239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.6
DANN	Benign	0.61
PhyloP100		-0.016

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs3811402; hg19: chr1-151119745;