7-22497105-C-G

Variant summary

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

The NM_001382447.1(STEAP1B):c.-31-2219G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.879 in 152,218 control chromosomes in the GnomAD database, including 58,888 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 0.88 (58888 hom., cov: 32)
• Consequence: STEAP1B NM_001382447.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.256

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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.923 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
STEAP1B	NM_001382447.1	c.-31-2219G>C		intron_variant		ENST00000678116.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STEAP1B	ENST00000678116.1	c.-31-2219G>C		intron_variant			NM_001382447.1	A2

Frequencies

GnomAD3 genomes AF: 0.879 AC: 133664 AN: 152100 Hom.: 58836 Cov.: 32

Gnomad AFR AF: 0.931

Gnomad AMI AF: 0.872

Gnomad AMR AF: 0.887

Gnomad ASJ AF: 0.880

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.861

Gnomad FIN AF: 0.820

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.855

Gnomad OTH AF: 0.896

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

GnomAD4 genome AF: 0.879 AC: 133773 AN: 152218 Hom.: 58888 Cov.: 32 AF XY: 0.878 AC XY: 65305 AN XY: 74412

Gnomad4 AFR AF: 0.931

Gnomad4 AMR AF: 0.886

Gnomad4 ASJ AF: 0.880

Gnomad4 EAS AF: 0.881

Gnomad4 SAS AF: 0.862

Gnomad4 FIN AF: 0.820

Gnomad4 NFE AF: 0.855

Gnomad4 OTH AF: 0.897

Alfa AF: 0.833 Hom.: 2540

Bravo AF: 0.885

Asia WGS AF: 0.881 AC: 3063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	5.6
Dann	Benign	0.60

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: rs4719697; hg19: chr7-22536724;