rs11631180

chr15-78082239-T-C

Variant summary

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

The ENST00000409568.6(SH2D7):c.-229+4301T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 152,094 control chromosomes in the GnomAD database, including 6,318 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 0.28 (6318 hom., cov: 32)
• Consequence: SH2D7 ENST00000409568.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.631

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SH2D7	ENST00000409568.6	c.-229+4301T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42442 AN: 151976 Hom.: 6311 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.0472

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.282

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

GnomAD4 genome AF: 0.279 AC: 42480 AN: 152094 Hom.: 6318 Cov.: 32 AF XY: 0.273 AC XY: 20302 AN XY: 74340

Gnomad4 AFR AF: 0.226

Gnomad4 AMR AF: 0.239

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.0474

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.336

Gnomad4 OTH AF: 0.286

Alfa AF: 0.328 Hom.: 15707

Bravo AF: 0.274

Asia WGS AF: 0.143 AC: 497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.19
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11631180; hg19: chr15-78374581;