chr11-16735326-C-G

Variant names:

• chr11-16735326-C-G
• rs11024028
• NM_001367872.1:c.-261+3099G>C

Variant summary

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

The NM_001367872.1(SOX6):​c.-261+3099G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.128 in 152,192 control chromosomes in the GnomAD database, including 1,619 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 0.13 (1619 hom., cov: 32)
• Consequence: SOX6 NM_001367872.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.117
• Publications: 8 publications found

Genes affected

SOX6 (HGNC:16421): (SRY-box transcription factor 6) This gene encodes a member of the D subfamily of sex determining region y-related transcription factors that are characterized by a conserved DNA-binding domain termed the high mobility group box and by their ability to bind the minor groove of DNA. The encoded protein is a transcriptional activator that is required for normal development of the central nervous system, chondrogenesis and maintenance of cardiac and skeletal muscle cells. The encoded protein interacts with other family members to cooperatively activate gene expression. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Mar 2009]

C11orf58 (HGNC:16990): (chromosome 11 open reading frame 58)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.191 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SOX6	NM_001367872.1	c.-261+3099G>C		intron_variant	Intron 1 of 16		NP_001354801.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOX6	ENST00000524520.5	n.353+1013G>C		intron_variant	Intron 2 of 5	5
SOX6	ENST00000525259.1	n.267+1013G>C		intron_variant	Intron 2 of 4	4
C11orf58	ENST00000527893.5	n.405-9275C>G		intron_variant	Intron 2 of 3	4
SOX6	ENST00000530378.5	n.-335+1013G>C		intron_variant	Intron 2 of 9	2		ENSP00000432577.1

Frequencies

GnomAD3 genomes AF: 0.128 AC: 19454 AN: 152076 Hom.: 1618 Cov.: 32

Gnomad AFR AF: 0.0358

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0557

Gnomad FIN AF: 0.136

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.128 AC: 19445 AN: 152192 Hom.: 1619 Cov.: 32 AF XY: 0.123 AC XY: 9187 AN XY: 74394

African (AFR) AF: 0.0357 AC: 1485 AN: 41548

American (AMR) AF: 0.125 AC: 1911 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 645 AN: 3470

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5188

South Asian (SAS) AF: 0.0547 AC: 264 AN: 4822

European-Finnish (FIN) AF: 0.136 AC: 1441 AN: 10582

Middle Eastern (MID) AF: 0.184 AC: 54 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13195 AN: 67980

Other (OTH) AF: 0.153 AC: 323 AN: 2108

Alfa AF: 0.162 Hom.: 277

Bravo AF: 0.124

Asia WGS AF: 0.0290 AC: 101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.19
DANN	Benign	0.57
PhyloP100		0.12

Splicing

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

Other links and lift over

dbSNP: rs11024028; hg19: chr11-16756873;