rs11758333

chr6-107524274-A-Cchr6-107524274-A-Gchr6-107524274-A-T

Variant summary

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

The NM_018013.4(SOBP):c.422-9185A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 152,068 control chromosomes in the GnomAD database, including 16,847 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 0.42 (16847 hom., cov: 32)
• Consequence: SOBP NM_018013.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167

Genes affected

SOBP (HGNC:29256): (sine oculis binding protein homolog) The protein encoded by this gene is a nuclear zinc finger protein that is involved in development of the cochlea. Defects in this gene have also been linked to intellectual disability. [provided by RefSeq, Mar 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.603 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SOBP	NM_018013.4	c.422-9185A>C		intron_variant		ENST00000317357.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SOBP	ENST00000317357.10	c.422-9185A>C		intron_variant		5	NM_018013.4	P1
SOBP	ENST00000477448.1	n.933-9185A>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.419 AC: 63743 AN: 151950 Hom.: 16843 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.266

Gnomad FIN AF: 0.487

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.608

Gnomad OTH AF: 0.481

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

GnomAD4 genome AF: 0.419 AC: 63745 AN: 152068 Hom.: 16847 Cov.: 32 AF XY: 0.408 AC XY: 30355 AN XY: 74338

Gnomad4 AFR AF: 0.131

Gnomad4 AMR AF: 0.415

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.101

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.487

Gnomad4 NFE AF: 0.608

Gnomad4 OTH AF: 0.483

Alfa AF: 0.508 Hom.: 9381

Bravo AF: 0.404

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	0.77
Dann	Benign	0.38
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs11758333; hg19: chr6-107845478; COSMIC: COSV58002351;