rs7762721

chr6-107545294-A-G

Variant summary

Our verdict is Benign. Variant got -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

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=-0.82).
• 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/exons	MANE	UniProt
SOBP	NM_018013.4	c.573+11684A>G		intron_variant		ENST00000317357.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SOBP	ENST00000317357.10	c.573+11684A>G		intron_variant		5	NM_018013.4	P1
SOBP	ENST00000477448.1	n.1084+11684A>G		intron_variant, non_coding_transcript_variant		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

Gnomad4 AFR AF: 0.870

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.426

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.738

Gnomad4 FIN AF: 0.512

Gnomad4 NFE AF: 0.400

Gnomad4 OTH AF: 0.523

Alfa AF: 0.463 Hom.: 8096

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

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: rs7762721; hg19: chr6-107866498;