chr9-112045361-A-G

Variant names:

• chr9-112045361-A-G
• rs7854368
• NM_022486.5:c.2150-3401T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 3 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=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.682 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_022486.5. 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
	SUSD1	NM_022486.5	MANE Select	c.2150-3401T>C		intron	N/A	NP_071931.2
	SUSD1	NM_001282640.2		c.2150-3196T>C		intron	N/A	NP_001269569.1	Q6UWL2-2
	SUSD1	NM_001282643.2		c.2110-3401T>C		intron	N/A	NP_001269572.1	F8WAQ1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SUSD1	ENST00000374270.8	TSL:1 MANE Select	c.2150-3401T>C		intron	N/A	ENSP00000363388.4	Q6UWL2-1
	SUSD1	ENST00000374264.6	TSL:1	c.2150-3196T>C		intron	N/A	ENSP00000363382.2	Q6UWL2-2
	SUSD1	ENST00000861057.1		c.2147-3401T>C		intron	N/A	ENSP00000531116.1

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

African (AFR) AF: 0.689 AC: 28527 AN: 41428

American (AMR) AF: 0.247 AC: 3766 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.229 AC: 793 AN: 3468

East Asian (EAS) AF: 0.421 AC: 2174 AN: 5160

South Asian (SAS) AF: 0.370 AC: 1781 AN: 4812

European-Finnish (FIN) AF: 0.320 AC: 3387 AN: 10580

Middle Eastern (MID) AF: 0.197 AC: 58 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13115 AN: 67994

Other (OTH) AF: 0.289 AC: 611 AN: 2116

Alfa AF: 0.232 Hom.: 8857

Bravo AF: 0.363

Asia WGS AF: 0.411 AC: 1427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	4.4
DANN	Benign	0.89
PhyloP100		-0.83
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: rs7854368; hg19: chr9-114807641; COSMIC: COSV62582822;