rs7995557

Positions:

• chr13-49928765-T-C

Variant summary

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

The NM_020456.4(SPRYD7):​c.224-680A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,116 control chromosomes in the GnomAD database, including 2,748 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 0.18 (2748 hom., cov: 32)
• Consequence: SPRYD7 NM_020456.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0710

Genes affected

SPRYD7 (HGNC:14297): (SPRY domain containing 7)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.259 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPRYD7	NM_020456.4	c.224-680A>G		intron_variant		ENST00000361840.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPRYD7	ENST00000361840.8	c.224-680A>G		intron_variant		1	NM_020456.4	P1
SPRYD7	ENST00000378195.6	c.107-680A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27015 AN: 151998 Hom.: 2739 Cov.: 32

Gnomad AFR AF: 0.263

Gnomad AMI AF: 0.0592

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.0316

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.187

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

GnomAD4 genome AF: 0.178 AC: 27062 AN: 152116 Hom.: 2748 Cov.: 32 AF XY: 0.177 AC XY: 13189 AN XY: 74358

Gnomad4 AFR AF: 0.263

Gnomad4 AMR AF: 0.126

Gnomad4 ASJ AF: 0.248

Gnomad4 EAS AF: 0.0318

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.185

Alfa AF: 0.169 Hom.: 357

Bravo AF: 0.174

Asia WGS AF: 0.0940 AC: 328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.9
DANN	Benign	0.52

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: rs7995557; hg19: chr13-50502901;