rs7854368

chr9-112045361-A-Gchr9-112045361-A-T

Variant summary

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

The NM_022486.5(SUSD1):c.2150-3401T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.358 in 152,032 control chromosomes in the GnomAD database, including 13,244 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 0.36 (13244 hom., cov: 32)
• Consequence: SUSD1 NM_022486.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.827

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SUSD1	NM_022486.5	c.2150-3401T>C		intron_variant		ENST00000374270.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SUSD1	ENST00000374270.8	c.2150-3401T>C		intron_variant		1	NM_022486.5	P2

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54263 AN: 151914 Hom.: 13190 Cov.: 32

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.229

Gnomad EAS AF: 0.422

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.203

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.358 AC: 54374 AN: 152032 Hom.: 13244 Cov.: 32 AF XY: 0.362 AC XY: 26889 AN XY: 74286

Gnomad4 AFR AF: 0.689

Gnomad4 AMR AF: 0.247

Gnomad4 ASJ AF: 0.229

Gnomad4 EAS AF: 0.421

Gnomad4 SAS AF: 0.370

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.193

Gnomad4 OTH AF: 0.289

Alfa AF: 0.218 Hom.: 6010

Bravo AF: 0.363

Asia WGS AF: 0.411 AC: 1427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	4.4
Dann	Benign	0.89

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: rs7854368; hg19: chr9-114807641; COSMIC: COSV62582822;