rs699699

chr6-107621148-G-Achr6-107621148-G-C

Variant summary

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

The NM_018013.4(SOBP):c.670-12366G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.987 in 850,542 control chromosomes in the GnomAD database, including 414,078 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 0.98 (73019 hom., cov: 33)
  • Exomes 𝑓: 0.99 (341059 hom.)
• Consequence: SOBP NM_018013.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.655

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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.982 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SOBP	NM_018013.4	c.670-12366G>A		intron_variant		ENST00000317357.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SOBP	ENST00000317357.10	c.670-12366G>A		intron_variant		5	NM_018013.4	P1

Frequencies

GnomAD3 genomes AF: 0.979 AC: 149018 AN: 152238 Hom.: 72960 Cov.: 33

Gnomad AFR AF: 0.955

Gnomad AMI AF: 1.00

Gnomad AMR AF: 0.978

Gnomad ASJ AF: 0.973

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.992

Gnomad FIN AF: 1.00

Gnomad MID AF: 0.962

Gnomad NFE AF: 0.988

Gnomad OTH AF: 0.968

GnomAD4 exome AF: 0.988 AC: 690049 AN: 698186 Hom.: 341059 Cov.: 8 AF XY: 0.988 AC XY: 320803 AN XY: 324582

Gnomad4 AFR exome AF: 0.952

Gnomad4 AMR exome AF: 0.983

Gnomad4 ASJ exome AF: 0.969

Gnomad4 EAS exome AF: 1.00

Gnomad4 SAS exome AF: 0.993

Gnomad4 FIN exome AF: 0.996

Gnomad4 NFE exome AF: 0.989

Gnomad4 OTH exome AF: 0.985

GnomAD4 genome AF: 0.979 AC: 149136 AN: 152356 Hom.: 73019 Cov.: 33 AF XY: 0.980 AC XY: 73035 AN XY: 74506

Gnomad4 AFR AF: 0.955

Gnomad4 AMR AF: 0.978

Gnomad4 ASJ AF: 0.973

Gnomad4 EAS AF: 1.00

Gnomad4 SAS AF: 0.993

Gnomad4 FIN AF: 1.00

Gnomad4 NFE AF: 0.988

Gnomad4 OTH AF: 0.969

Alfa AF: 0.984 Hom.: 8945

Bravo AF: 0.976

Asia WGS AF: 0.993 AC: 3453 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
Cadd	Benign	12
Dann	Benign	0.74

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		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: rs699699; hg19: chr6-107942352;