chr15-82784743-A-G

Variant names:

• chr15-82784743-A-G
• rs7163402
• NM_001007122.4:c.736-1718T>C

Variant summary

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

The NM_001007122.4(FSD2):​c.736-1718T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.838 in 152,120 control chromosomes in the GnomAD database, including 53,965 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 0.84 (53965 hom., cov: 30)
• Consequence: FSD2 NM_001007122.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0100
• Publications: 9 publications found

Genes affected

FSD2 (HGNC:18024): (fibronectin type III and SPRY domain containing 2) This gene encodes a protein that belongs to the FN3/SPRY family of proteins. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]

SNHG21 (HGNC:50284): (small nucleolar RNA host gene 21)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.946 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001007122.4. 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
	FSD2	NM_001007122.4	MANE Select	c.736-1718T>C		intron	N/A	NP_001007123.1	A1L4K1-1
	FSD2	NM_001281805.2		c.736-1718T>C		intron	N/A	NP_001268734.1	A1L4K1-2
	FSD2	NM_001281806.2		c.736-1718T>C		intron	N/A	NP_001268735.1	A1L4K1-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	FSD2	ENST00000334574.12	TSL:1 MANE Select	c.736-1718T>C		intron	N/A	ENSP00000335651.8	A1L4K1-1
	FSD2	ENST00000541889.1	TSL:1	c.736-1718T>C		intron	N/A	ENSP00000444078.1	A1L4K1-2
	FSD2	ENST00000961201.1		c.736-1718T>C		intron	N/A	ENSP00000631260.1

Frequencies

GnomAD3 genomes AF: 0.838 AC: 127428 AN: 152002 Hom.: 53898 Cov.: 30

Gnomad AFR AF: 0.954

Gnomad AMI AF: 0.666

Gnomad AMR AF: 0.866

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.851

Gnomad SAS AF: 0.630

Gnomad FIN AF: 0.793

Gnomad MID AF: 0.774

Gnomad NFE AF: 0.787

Gnomad OTH AF: 0.830

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

GnomAD4 genome AF: 0.838 AC: 127551 AN: 152120 Hom.: 53965 Cov.: 30 AF XY: 0.835 AC XY: 62117 AN XY: 74352

African (AFR) AF: 0.954 AC: 39605 AN: 41514

American (AMR) AF: 0.866 AC: 13238 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.804 AC: 2790 AN: 3470

East Asian (EAS) AF: 0.851 AC: 4397 AN: 5166

South Asian (SAS) AF: 0.630 AC: 3032 AN: 4810

European-Finnish (FIN) AF: 0.793 AC: 8395 AN: 10582

Middle Eastern (MID) AF: 0.764 AC: 223 AN: 292

European-Non Finnish (NFE) AF: 0.787 AC: 53509 AN: 67978

Other (OTH) AF: 0.831 AC: 1757 AN: 2114

Alfa AF: 0.798 Hom.: 38194

Bravo AF: 0.854

Asia WGS AF: 0.787 AC: 2736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.6
DANN	Benign	0.30
PhyloP100		0.010
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs7163402; hg19: chr15-83453495;