rs17364464

Positions:

• chr7-22474434-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.762+18131T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 152,236 control chromosomes in the GnomAD database, including 1,216 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 0.12 (1216 hom., cov: 32)
• Consequence: STEAP1B NM_001382447.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133

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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.143 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STEAP1B	NM_001382447.1	c.762+18131T>C		intron_variant		ENST00000678116.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STEAP1B	ENST00000678116.1	c.762+18131T>C		intron_variant			NM_001382447.1	A2
STEAP1B	ENST00000404369.8	c.762+18131T>C		intron_variant		1		A2
STEAP1B	ENST00000406890.6	c.705+18131T>C		intron_variant		1		P2

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18646 AN: 152118 Hom.: 1210 Cov.: 32

Gnomad AFR AF: 0.0831

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.110

Gnomad ASJ AF: 0.0991

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.110

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.0860

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.102

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

GnomAD4 genome AF: 0.123 AC: 18671 AN: 152236 Hom.: 1216 Cov.: 32 AF XY: 0.122 AC XY: 9106 AN XY: 74436

Gnomad4 AFR AF: 0.0835

Gnomad4 AMR AF: 0.110

Gnomad4 ASJ AF: 0.0991

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.102

Alfa AF: 0.140 Hom.: 2361

Bravo AF: 0.118

Asia WGS AF: 0.134 AC: 467 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
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: rs17364464; hg19: chr7-22514053;