NM_022486.5:c.1475-7745G>A

Variant names:

• chr9-112087910-C-T
• rs2782931
• NM_022486.5:c.1475-7745G>A

Variant summary

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

The NM_022486.5(SUSD1):​c.1475-7745G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 151,924 control chromosomes in the GnomAD database, including 5,995 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 0.28 (5995 hom., cov: 32)
• Consequence: SUSD1 NM_022486.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.151

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=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUSD1	NM_022486.5	c.1475-7745G>A		intron_variant	Intron 10 of 16	ENST00000374270.8	NP_071931.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUSD1	ENST00000374270.8	c.1475-7745G>A		intron_variant	Intron 10 of 16	1	NM_022486.5	ENSP00000363388.4

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41800 AN: 151806 Hom.: 5985 Cov.: 32

Gnomad AFR AF: 0.220

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.263

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

GnomAD4 genome AF: 0.275 AC: 41849 AN: 151924 Hom.: 5995 Cov.: 32 AF XY: 0.271 AC XY: 20136 AN XY: 74254

Gnomad4 AFR AF: 0.220

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.223

Gnomad4 SAS AF: 0.208

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.324

Gnomad4 OTH AF: 0.265

Alfa AF: 0.310 Hom.: 15942

Bravo AF: 0.272

Asia WGS AF: 0.224 AC: 777 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.2
DANN	Benign	0.43

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: rs2782931; hg19: chr9-114850190;