rs1320464

Variant names:

• chr9-38019804-C-A
• rs1320464
• NM_003028.3:c.718-3673G>T

Your query was ambiguous. Multiple possible variants found:

• chr9-38019804-C-A
• chr9-38019804-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_003028.3(SHB):​c.718-3673G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 152,034 control chromosomes in the GnomAD database, including 6,539 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 0.29 (6539 hom., cov: 33)
• Consequence: SHB NM_003028.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.360
• Publications: 2 publications found

Genes affected

SHB (HGNC:10838): (SH2 domain containing adaptor protein B) Enables phosphotyrosine residue binding activity. Predicted to be involved in several processes, including angiogenesis; apoptotic process; and signal transduction. Predicted to act upstream of or within several processes, including hematopoietic stem cell proliferation; negative regulation of oocyte maturation; and positive regulation of immune response. Located in cytoplasmic ribonucleoprotein granule; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000255872 (HGNC:):

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 (AMR) allele frequency at 95% confidence interval = 0.302 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SHB	NM_003028.3	c.718-3673G>T		intron_variant	Intron 1 of 5	ENST00000377707.4	NP_003019.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SHB	ENST00000377707.4	c.718-3673G>T		intron_variant	Intron 1 of 5	1	NM_003028.3	ENSP00000366936.3
ENSG00000255872	ENST00000540557.1	n.718-3673G>T		intron_variant	Intron 1 of 11	5		ENSP00000457548.1

Frequencies

GnomAD3 genomes AF: 0.289 AC: 43918 AN: 151916 Hom.: 6532 Cov.: 33

Gnomad AFR AF: 0.295

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.431

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.420

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.291

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

GnomAD4 genome AF: 0.289 AC: 43959 AN: 152034 Hom.: 6539 Cov.: 33 AF XY: 0.287 AC XY: 21343 AN XY: 74346

African (AFR) AF: 0.295 AC: 12239 AN: 41442

American (AMR) AF: 0.309 AC: 4728 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.431 AC: 1494 AN: 3470

East Asian (EAS) AF: 0.161 AC: 831 AN: 5168

South Asian (SAS) AF: 0.255 AC: 1227 AN: 4814

European-Finnish (FIN) AF: 0.222 AC: 2345 AN: 10574

Middle Eastern (MID) AF: 0.414 AC: 121 AN: 292

European-Non Finnish (NFE) AF: 0.297 AC: 20208 AN: 67972

Other (OTH) AF: 0.287 AC: 603 AN: 2102

Alfa AF: 0.213 Hom.: 564

Bravo AF: 0.297

Asia WGS AF: 0.160 AC: 558 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	0.69
DANN	Benign	0.56
PhyloP100		-0.36
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: rs1320464; hg19: chr9-38019801;