rs740295

chr7-22433669-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001382447.1(STEAP1B):c.763-13833T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.241 in 152,146 control chromosomes in the GnomAD database, including 5,399 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 0.24 (5399 hom., cov: 31)
• Consequence: STEAP1B NM_001382447.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890

Genes affected

STEAP1B (HGNC:41907): (STEAP family member 1B) Predicted to be integral component of membrane. Predicted to be active in endosome and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STEAP1B	NM_001382447.1	c.763-13833T>C		intron_variant		ENST00000678116.1
STEAP1B	NM_207342.3	c.706-13833T>C		intron_variant
STEAP1B	XM_047420107.1	c.826-13833T>C		intron_variant
STEAP1B	XM_047420109.1	c.769-13833T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STEAP1B	ENST00000678116.1	c.763-13833T>C		intron_variant			NM_001382447.1	A2
STEAP1B	ENST00000406890.6	c.706-13833T>C		intron_variant		1		P2

Frequencies

GnomAD3 genomes AF: 0.241 AC: 36657 AN: 152028 Hom.: 5392 Cov.: 31

Gnomad AFR AF: 0.0913

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.232

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.432

Gnomad MID AF: 0.159

Gnomad NFE AF: 0.312

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.241 AC: 36697 AN: 152146 Hom.: 5399 Cov.: 31 AF XY: 0.245 AC XY: 18188 AN XY: 74374

Gnomad4 AFR AF: 0.0915

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.232

Gnomad4 EAS AF: 0.116

Gnomad4 SAS AF: 0.169

Gnomad4 FIN AF: 0.432

Gnomad4 NFE AF: 0.312

Gnomad4 OTH AF: 0.199

Alfa AF: 0.276 Hom.: 1910

Bravo AF: 0.221

Asia WGS AF: 0.140 AC: 484 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	3.4
Dann	Benign	0.45

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: rs740295; hg19: chr7-22473288;