rs11631180

Variant names:

• chr15-78082239-T-C
• rs11631180
• ENST00000409568.6:c.-229+4301T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SH2D7	ENST00000409568.6	c.-229+4301T>C		intron_variant	Intron 1 of 5	5		ENSP00000386676.2

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

African (AFR) AF: 0.226 AC: 9391 AN: 41480

American (AMR) AF: 0.239 AC: 3654 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1412 AN: 3468

East Asian (EAS) AF: 0.0474 AC: 245 AN: 5174

South Asian (SAS) AF: 0.219 AC: 1054 AN: 4820

European-Finnish (FIN) AF: 0.274 AC: 2899 AN: 10570

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.336 AC: 22846 AN: 67982

Other (OTH) AF: 0.286 AC: 603 AN: 2112

Alfa AF: 0.320 Hom.: 30898

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
PhyloP100		-0.63
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs11631180; hg19: chr15-78374581;