rs7995557

Variant names:

• chr13-49928765-T-C
• rs7995557
• NM_020456.4:c.224-680A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SPRYD7	NM_020456.4	c.224-680A>G		intron_variant	Intron 2 of 4	ENST00000361840.8	NP_065189.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPRYD7	ENST00000361840.8	c.224-680A>G		intron_variant	Intron 2 of 4	1	NM_020456.4	ENSP00000354774.3
SPRYD7	ENST00000378195.6	c.107-680A>G		intron_variant	Intron 1 of 3	2		ENSP00000367437.2

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

African (AFR) AF: 0.263 AC: 10902 AN: 41468

American (AMR) AF: 0.126 AC: 1925 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 859 AN: 3470

East Asian (EAS) AF: 0.0318 AC: 165 AN: 5186

South Asian (SAS) AF: 0.141 AC: 678 AN: 4814

European-Finnish (FIN) AF: 0.202 AC: 2141 AN: 10576

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9901 AN: 68002

Other (OTH) AF: 0.185 AC: 391 AN: 2112

Alfa AF: 0.173 Hom.: 387

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
PhyloP100		0.071
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: rs7995557; hg19: chr13-50502901;