rs10401969

Variant names:

• chr19-19296909-T-C
• rs10401969
• NM_172231.4:c.1243+80A>G

Variant summary

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

The NM_172231.4(SUGP1):​c.1243+80A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0812 in 1,198,724 control chromosomes in the GnomAD database, including 4,332 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 0.10 (931 hom., cov: 32)
  • Exomes 𝑓: 0.078 (3401 hom.)
• Consequence: SUGP1 NM_172231.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.240
• Publications: 260 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_172231.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUGP1	NM_172231.4	MANE Select	c.1243+80A>G		intron	N/A	NP_757386.2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUGP1	ENST00000247001.10	TSL:1 MANE Select	c.1243+80A>G		intron	N/A	ENSP00000247001.3	Q8IWZ8-1
	SUGP1	ENST00000588731.6	TSL:1	n.*770+80A>G		intron	N/A	ENSP00000465413.2	Q8IWZ8-2
	SUGP1	ENST00000589144.5	TSL:1	n.*506+80A>G		intron	N/A	ENSP00000466402.3	K7EM86

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15248 AN: 152094 Hom.: 916 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.114

Gnomad AMR AF: 0.0717

Gnomad ASJ AF: 0.0475

Gnomad EAS AF: 0.0993

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0579

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0738

Gnomad OTH AF: 0.0823

GnomAD4 exome AF: 0.0784 AC: 82017 AN: 1046512 Hom.: 3401 AF XY: 0.0784 AC XY: 40447 AN XY: 515740

African (AFR) AF: 0.170 AC: 4089 AN: 23992

American (AMR) AF: 0.0531 AC: 1129 AN: 21264

Ashkenazi Jewish (ASJ) AF: 0.0543 AC: 935 AN: 17210

East Asian (EAS) AF: 0.101 AC: 3450 AN: 34266

South Asian (SAS) AF: 0.0976 AC: 5586 AN: 57254

European-Finnish (FIN) AF: 0.0625 AC: 2213 AN: 35394

Middle Eastern (MID) AF: 0.0529 AC: 165 AN: 3120

European-Non Finnish (NFE) AF: 0.0753 AC: 60888 AN: 808508

Other (OTH) AF: 0.0783 AC: 3562 AN: 45504

GnomAD4 genome AF: 0.101 AC: 15301 AN: 152212 Hom.: 931 Cov.: 32 AF XY: 0.0998 AC XY: 7428 AN XY: 74436

African (AFR) AF: 0.171 AC: 7087 AN: 41524

American (AMR) AF: 0.0716 AC: 1094 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0475 AC: 165 AN: 3472

East Asian (EAS) AF: 0.0991 AC: 513 AN: 5174

South Asian (SAS) AF: 0.102 AC: 494 AN: 4830

European-Finnish (FIN) AF: 0.0579 AC: 615 AN: 10614

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0738 AC: 5018 AN: 67998

Other (OTH) AF: 0.0900 AC: 190 AN: 2112

Alfa AF: 0.0829 Hom.: 2595

Bravo AF: 0.105

Asia WGS AF: 0.140 AC: 487 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.2
DANN	Benign	0.73
PhyloP100		0.24
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: rs10401969; hg19: chr19-19407718;