rs17107469

Positions:

• chr10-80646491-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001388272.1(SH2D4B):​c.*2406T>C variant causes a 3 prime UTR change. The variant allele was found at a frequency of 0.0386 in 152,238 control chromosomes in the GnomAD database, including 265 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 0.039 (265 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: SH2D4B NM_001388272.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.71

Genes affected

SH2D4B (HGNC:31440): (SH2 domain containing 4B) Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

LOC105378387 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.2).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.109 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SH2D4B	NM_001388272.1	c.*2406T>C		3_prime_UTR_variant	8/8	ENST00000646907.2
LOC105378387	XR_946132.1	n.225+2628A>G		intron_variant, non_coding_transcript_variant
SH2D4B	NM_001145719.1	c.*2410T>C		3_prime_UTR_variant	7/7
SH2D4B	NM_207372.2	c.*2410T>C		3_prime_UTR_variant	7/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SH2D4B	ENST00000646907.2	c.*2406T>C		3_prime_UTR_variant	8/8		NM_001388272.1	P1
SH2D4B	ENST00000339284.6	c.*2410T>C		3_prime_UTR_variant	7/7	2
SH2D4B	ENST00000372150.7	n.2829T>C		non_coding_transcript_exon_variant	3/3	5
SH2D4B	ENST00000481537.1	n.2559T>C		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.0386 AC: 5871 AN: 152120 Hom.: 263 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0193

Gnomad ASJ AF: 0.0262

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0163

Gnomad FIN AF: 0.00141

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00991

Gnomad OTH AF: 0.0382

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.0386 AC: 5882 AN: 152238 Hom.: 265 Cov.: 32 AF XY: 0.0367 AC XY: 2735 AN XY: 74436

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.0193

Gnomad4 ASJ AF: 0.0262

Gnomad4 EAS AF: 0.00135

Gnomad4 SAS AF: 0.0162

Gnomad4 FIN AF: 0.00141

Gnomad4 NFE AF: 0.00991

Gnomad4 OTH AF: 0.0378

Alfa AF: 0.0273 Hom.: 26

Bravo AF: 0.0436

Asia WGS AF: 0.0180 AC: 64 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.20
CADD	Benign	17
DANN	Benign	0.91

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: rs17107469; hg19: chr10-82406247;