rs7762721

Variant names:

• chr6-107545294-A-G
• rs7762721
• NM_018013.4:c.573+11684A>G

Variant summary

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

The NM_018013.4(SOBP):​c.573+11684A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.586 in 152,086 control chromosomes in the GnomAD database, including 29,532 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 (29532 hom., cov: 32)
• Consequence: SOBP NM_018013.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.192
• Publications: 3 publications found

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]

SOBP Gene-Disease associations (from GenCC):

• intellectual disability, anterior maxillary protrusion, and strabismus

  Inheritance: Unknown, AR Classification: SUPPORTIVE, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), G2P, Orphanet
• syndromic intellectual disability

  Inheritance: AR Classification: LIMITED Submitted by: ClinGen

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 (EAS) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SOBP	NM_018013.4	c.573+11684A>G		intron_variant	Intron 4 of 6	ENST00000317357.10	NP_060483.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SOBP	ENST00000317357.10	c.573+11684A>G		intron_variant	Intron 4 of 6	5	NM_018013.4	ENSP00000318900.5
SOBP	ENST00000477448.1	n.1084+11684A>G		intron_variant	Intron 4 of 4	5

Frequencies

GnomAD3 genomes AF: 0.586 AC: 88981 AN: 151968 Hom.: 29471 Cov.: 32

Gnomad AFR AF: 0.870

Gnomad AMI AF: 0.496

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.426

Gnomad EAS AF: 0.899

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.512

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.400

Gnomad OTH AF: 0.525

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

GnomAD4 genome AF: 0.586 AC: 89098 AN: 152086 Hom.: 29532 Cov.: 32 AF XY: 0.597 AC XY: 44336 AN XY: 74324

African (AFR) AF: 0.870 AC: 36129 AN: 41512

American (AMR) AF: 0.592 AC: 9046 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.426 AC: 1477 AN: 3468

East Asian (EAS) AF: 0.899 AC: 4651 AN: 5172

South Asian (SAS) AF: 0.738 AC: 3554 AN: 4814

European-Finnish (FIN) AF: 0.512 AC: 5414 AN: 10568

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.400 AC: 27170 AN: 67952

Other (OTH) AF: 0.523 AC: 1106 AN: 2114

Alfa AF: 0.459 Hom.: 8818

Bravo AF: 0.601

Asia WGS AF: 0.815 AC: 2830 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	9.5
DANN	Benign	0.55
PhyloP100		0.19
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: rs7762721; hg19: chr6-107866498;