9-112126236-T-C

Variant names:

• chr9-112126236-T-C
• rs2762475
• NM_022486.5:c.707-1800A>G

Variant summary

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

The NM_022486.5(SUSD1):​c.707-1800A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 151,894 control chromosomes in the GnomAD database, including 14,679 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 0.43 (14679 hom., cov: 32)
• Consequence: SUSD1 NM_022486.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.860
• Publications: 4 publications found

Genes affected

SUSD1 (HGNC:25413): (sushi domain containing 1) Predicted to enable calcium ion binding activity. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUSD1	NM_022486.5	c.707-1800A>G		intron_variant	Intron 5 of 16	ENST00000374270.8	NP_071931.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUSD1	ENST00000374270.8	c.707-1800A>G		intron_variant	Intron 5 of 16	1	NM_022486.5	ENSP00000363388.4

Frequencies

GnomAD3 genomes AF: 0.432 AC: 65618 AN: 151774 Hom.: 14654 Cov.: 32

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.248

Gnomad AMR AF: 0.449

Gnomad ASJ AF: 0.363

Gnomad EAS AF: 0.652

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.482

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.369

Gnomad OTH AF: 0.428

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.433 AC: 65696 AN: 151894 Hom.: 14679 Cov.: 32 AF XY: 0.441 AC XY: 32742 AN XY: 74240

African (AFR) AF: 0.478 AC: 19791 AN: 41416

American (AMR) AF: 0.450 AC: 6865 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.363 AC: 1259 AN: 3466

East Asian (EAS) AF: 0.652 AC: 3366 AN: 5160

South Asian (SAS) AF: 0.629 AC: 3032 AN: 4822

European-Finnish (FIN) AF: 0.482 AC: 5076 AN: 10528

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.369 AC: 25033 AN: 67920

Other (OTH) AF: 0.435 AC: 916 AN: 2106

Alfa AF: 0.390 Hom.: 51258

Bravo AF: 0.430

Asia WGS AF: 0.641 AC: 2227 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.12
DANN	Benign	0.68
PhyloP100		-0.86
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: rs2762475; hg19: chr9-114888516;