rs17750998

chr19-19277637-G-Achr19-19277637-G-T

Variant summary

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

The NM_172231.4(SUGP1):c.1781+97C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0654 in 1,473,280 control chromosomes in the GnomAD database, including 3,685 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 0.053 (353 hom., cov: 32)
  • Exomes 𝑓: 0.067 (3332 hom.)
• Consequence: SUGP1 NM_172231.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55

Genes affected

SUGP1 (HGNC:18643): (SURP and G-patch domain containing 1) SF4 is a member of the SURP family of splicing factors.[supplied by OMIM, Sep 2003]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0757 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SUGP1	NM_172231.4	c.1781+97C>T		intron_variant		ENST00000247001.10
SUGP1	XM_047439142.1	c.1151+97C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SUGP1	ENST00000247001.10	c.1781+97C>T		intron_variant		1	NM_172231.4	P1

Frequencies

GnomAD3 genomes AF: 0.0534 AC: 8129 AN: 152092 Hom.: 354 Cov.: 32

Gnomad AFR AF: 0.0123

Gnomad AMI AF: 0.0439

Gnomad AMR AF: 0.0299

Gnomad ASJ AF: 0.0620

Gnomad EAS AF: 0.000771

Gnomad SAS AF: 0.0522

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0775

Gnomad OTH AF: 0.0397

GnomAD4 exome AF: 0.0668 AC: 88215 AN: 1321070 Hom.: 3332 AF XY: 0.0672 AC XY: 43722 AN XY: 650562

Gnomad4 AFR exome AF: 0.00933

Gnomad4 AMR exome AF: 0.0242

Gnomad4 ASJ exome AF: 0.0665

Gnomad4 EAS exome AF: 0.000319

Gnomad4 SAS exome AF: 0.0650

Gnomad4 FIN exome AF: 0.119

Gnomad4 NFE exome AF: 0.0708

Gnomad4 OTH exome AF: 0.0642

GnomAD4 genome AF: 0.0534 AC: 8123 AN: 152210 Hom.: 353 Cov.: 32 AF XY: 0.0554 AC XY: 4121 AN XY: 74424

Gnomad4 AFR AF: 0.0122

Gnomad4 AMR AF: 0.0298

Gnomad4 ASJ AF: 0.0620

Gnomad4 EAS AF: 0.000772

Gnomad4 SAS AF: 0.0520

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.0774

Gnomad4 OTH AF: 0.0388

Alfa AF: 0.0620 Hom.: 267

Bravo AF: 0.0428

Asia WGS AF: 0.0230 AC: 79 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.099
Dann	Benign	0.46

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: rs17750998; hg19: chr19-19388446;