15-78089318-C-G

Variant names:

• chr15-78089318-C-G
• rs4473152
• ENST00000409568.6:c.-228-4798C>G

Variant summary

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

The ENST00000409568.6(SH2D7):​c.-228-4798C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 151,890 control chromosomes in the GnomAD database, including 6,054 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 0.26 (6054 hom., cov: 32)
• Consequence: SH2D7 ENST00000409568.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.109

Genes affected

SH2D7 (HGNC:34549): (SH2 domain containing 7)

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 = 0.347 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SH2D7	ENST00000409568.6	c.-228-4798C>G		intron_variant	Intron 1 of 5	5		ENSP00000386676.2

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40178 AN: 151772 Hom.: 6049 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.301

Gnomad AMR AF: 0.248

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.0503

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.272

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

GnomAD4 genome AF: 0.265 AC: 40212 AN: 151890 Hom.: 6054 Cov.: 32 AF XY: 0.259 AC XY: 19245 AN XY: 74220

Gnomad4 AFR AF: 0.142

Gnomad4 AMR AF: 0.248

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.0504

Gnomad4 SAS AF: 0.237

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.275

Alfa AF: 0.176 Hom.: 392

Bravo AF: 0.258

Asia WGS AF: 0.152 AC: 527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs4473152; hg19: chr15-78381660;