chr10-80646491-T-C

Variant names:

• chr10-80646491-T-C
• rs17107469
• NM_001388272.1:c.*2406T>C

Variant summary

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

Genes affected

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

ENSG00000298970 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SH2D4B	NM_001388272.1	c.*2406T>C		3_prime_UTR_variant	Exon 8 of 8	ENST00000646907.2	NP_001375201.1
SH2D4B	NM_207372.2	c.*2410T>C		3_prime_UTR_variant	Exon 7 of 7		NP_997255.2
SH2D4B	NM_001145719.1	c.*2410T>C		3_prime_UTR_variant	Exon 7 of 7		NP_001139191.1
LOC105378387	XR_946132.1	n.225+2628A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SH2D4B	ENST00000646907.2	c.*2406T>C		3_prime_UTR_variant	Exon 8 of 8		NM_001388272.1	ENSP00000494732.1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.112 AC: 4634 AN: 41520

American (AMR) AF: 0.0193 AC: 295 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0262 AC: 91 AN: 3472

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5176

South Asian (SAS) AF: 0.0162 AC: 78 AN: 4828

European-Finnish (FIN) AF: 0.00141 AC: 15 AN: 10606

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00991 AC: 674 AN: 68014

Other (OTH) AF: 0.0378 AC: 80 AN: 2116

Alfa AF: 0.0298 Hom.: 29

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
PhyloP100		4.7
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: rs17107469; hg19: chr10-82406247;