rs193573

Positions:

• chr7-117198257-G-A
• chr7-117198257-G-C
• chr7-117198257-G-T

Variant summary

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

The NM_001369598.1(ST7):​c.1254+7321G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.676 in 448,512 control chromosomes in the GnomAD database, including 104,320 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 0.64 (32153 hom., cov: 32)
  • Exomes 𝑓: 0.69 (72167 hom.)
• Consequence: ST7 NM_001369598.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

Genes affected

ST7 (HGNC:11351): (suppression of tumorigenicity 7) The gene for this product maps to a region on chromosome 7 identified as an autism-susceptibility locus. Mutation screening of the entire coding region in autistic individuals failed to identify phenotype-specific variants, suggesting that coding mutations for this gene are unlikely to be involved in the etiology of autism. The function of this gene product has not been determined. Transcript variants encoding different isoforms of this protein have been described. [provided by RefSeq, Jul 2008]

ST7-OT3 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ST7	NM_001369598.1	c.1254+7321G>A		intron_variant		ENST00000323984.8
ST7-OT3	NR_002332.2	n.580-63G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ST7	ENST00000323984.8	c.1254+7321G>A		intron_variant		5	NM_001369598.1

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97871 AN: 151992 Hom.: 32130 Cov.: 32

Gnomad AFR AF: 0.547

Gnomad AMI AF: 0.689

Gnomad AMR AF: 0.759

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.765

Gnomad FIN AF: 0.557

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.651

Gnomad OTH AF: 0.689

GnomAD4 exome AF: 0.692 AC: 205129 AN: 296402 Hom.: 72167 AF XY: 0.699 AC XY: 118102 AN XY: 168850

Gnomad4 AFR exome AF: 0.547

Gnomad4 AMR exome AF: 0.822

Gnomad4 ASJ exome AF: 0.787

Gnomad4 EAS exome AF: 0.930

Gnomad4 SAS exome AF: 0.751

Gnomad4 FIN exome AF: 0.563

Gnomad4 NFE exome AF: 0.646

Gnomad4 OTH exome AF: 0.689

GnomAD4 genome AF: 0.644 AC: 97947 AN: 152110 Hom.: 32153 Cov.: 32 AF XY: 0.647 AC XY: 48132 AN XY: 74356

Gnomad4 AFR AF: 0.547

Gnomad4 AMR AF: 0.760

Gnomad4 ASJ AF: 0.790

Gnomad4 EAS AF: 0.924

Gnomad4 SAS AF: 0.765

Gnomad4 FIN AF: 0.557

Gnomad4 NFE AF: 0.651

Gnomad4 OTH AF: 0.690

Alfa AF: 0.665 Hom.: 33694

Bravo AF: 0.656

Asia WGS AF: 0.825 AC: 2869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.053
DANN	Benign	0.56

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: rs193573; hg19: chr7-116838311;