rs148470229

Variant names:

• chr10-80603625-G-A
• rs148470229
• NM_001388272.1:c.690G>A

Your query was ambiguous. Multiple possible variants found:

• chr10-80603625-G-A
• chr10-80603625-G-C
• chr10-80603625-G-T

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_Moderate BP7 BS2

The NM_001388272.1(SH2D4B):​c.690G>A​(p.Gln230Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00066 in 1,588,602 control chromosomes in the GnomAD database, including 6 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 0.0034 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00037 (6 hom.)
• Consequence: SH2D4B NM_001388272.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.37

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -7 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BP7: Synonymous conserved (PhyloP=1.37 with no splicing effect.
• BS2: High Homozygotes in GnomAdExome4 at 6 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SH2D4B	NM_001388272.1	c.690G>A	p.Gln230Gln	synonymous_variant	Exon 5 of 8	ENST00000646907.2	NP_001375201.1
SH2D4B	NM_207372.2	c.690G>A	p.Gln230Gln	synonymous_variant	Exon 5 of 7		NP_997255.2
SH2D4B	NM_001145719.1	c.543G>A	p.Gln181Gln	synonymous_variant	Exon 5 of 7		NP_001139191.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SH2D4B	ENST00000646907.2	c.690G>A	p.Gln230Gln	synonymous_variant	Exon 5 of 8		NM_001388272.1	ENSP00000494732.1
SH2D4B	ENST00000339284.6	c.690G>A	p.Gln230Gln	synonymous_variant	Exon 5 of 7	2		ENSP00000345295.2
SH2D4B	ENST00000313455.5	c.543G>A	p.Gln181Gln	synonymous_variant	Exon 5 of 7	2		ENSP00000314242.4

Frequencies

GnomAD3 genomes AF: 0.00338 AC: 515 AN: 152232 Hom.: 0 Cov.: 33

Gnomad AFR AF: 0.0121

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000654

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000147

Gnomad OTH AF: 0.00191

GnomAD3 exomes AF: 0.000950 AC: 197 AN: 207352 Hom.: 1 AF XY: 0.000697 AC XY: 78 AN XY: 111944

Gnomad AFR exome AF: 0.0143

Gnomad AMR exome AF: 0.000474

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000110

Gnomad OTH exome AF: 0.000764

GnomAD4 exome AF: 0.000372 AC: 535 AN: 1436252 Hom.: 6 Cov.: 34 AF XY: 0.000320 AC XY: 228 AN XY: 711994

Gnomad4 AFR exome AF: 0.0133

Gnomad4 AMR exome AF: 0.000546

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000121

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000164

Gnomad4 OTH exome AF: 0.000858

GnomAD4 genome AF: 0.00337 AC: 514 AN: 152350 Hom.: 0 Cov.: 33 AF XY: 0.00340 AC XY: 253 AN XY: 74500

Gnomad4 AFR AF: 0.0120

Gnomad4 AMR AF: 0.000653

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000147

Gnomad4 OTH AF: 0.00189

Alfa AF: 0.00106 Hom.: 0

Bravo AF: 0.00405

Asia WGS AF: 0.000289 AC: 1 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
CADD	Benign	5.6
DANN	Benign	0.82

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: rs148470229; hg19: chr10-82363381;