rs4678778

Variant names:

• chr3-33215942-A-G
• rs4678778
• NM_015551.2:c.113-1837T>C

Variant summary

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

The NM_015551.2(SUSD5):​c.113-1837T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,168 control chromosomes in the GnomAD database, including 2,150 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 0.14 (2150 hom., cov: 32)
• Consequence: SUSD5 NM_015551.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0170
• Publications: 2 publications found

Genes affected

SUSD5 (HGNC:29061): (sushi domain containing 5) Predicted to enable hyaluronic acid binding activity. Predicted to be involved in Notch signaling pathway. 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=-0.47).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SUSD5	NM_015551.2	c.113-1837T>C		intron_variant	Intron 1 of 4	ENST00000309558.8	NP_056366.1
SUSD5	XM_005265034.4	c.113-1837T>C		intron_variant	Intron 1 of 3		XP_005265091.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SUSD5	ENST00000309558.8	c.113-1837T>C		intron_variant	Intron 1 of 4	1	NM_015551.2	ENSP00000308727.3
SUSD5	ENST00000412539.1	c.107-1837T>C		intron_variant	Intron 1 of 3	3		ENSP00000406475.1

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20856 AN: 152050 Hom.: 2133 Cov.: 32

Gnomad AFR AF: 0.0760

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.236

Gnomad FIN AF: 0.233

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.137 AC: 20893 AN: 152168 Hom.: 2150 Cov.: 32 AF XY: 0.147 AC XY: 10960 AN XY: 74400

African (AFR) AF: 0.0758 AC: 3150 AN: 41548

American (AMR) AF: 0.300 AC: 4579 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.101 AC: 351 AN: 3470

East Asian (EAS) AF: 0.342 AC: 1774 AN: 5180

South Asian (SAS) AF: 0.237 AC: 1140 AN: 4818

European-Finnish (FIN) AF: 0.233 AC: 2464 AN: 10580

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.103 AC: 7035 AN: 67980

Other (OTH) AF: 0.157 AC: 331 AN: 2106

Alfa AF: 0.113 Hom.: 1772

Bravo AF: 0.141

Asia WGS AF: 0.344 AC: 1192 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	7.9
DANN	Benign	0.94
PhyloP100		-0.017
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: rs4678778; hg19: chr3-33257434;