chr7-22608575-G-A

Variant names:

• chr7-22608575-G-A
• rs2905308
• ENST00000442252.1:n.129-35815C>T

Variant summary

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

The ENST00000439708.1(STEAP1B):​c.-32+24235C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.488 in 152,026 control chromosomes in the GnomAD database, including 19,952 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 0.49 (19952 hom., cov: 32)
• Consequence: STEAP1B ENST00000439708.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537

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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.618 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STEAP1B	ENST00000442252.1	n.129-35815C>T		intron_variant	Intron 1 of 1	1
STEAP1B	ENST00000439708.1	c.-32+24235C>T		intron_variant	Intron 1 of 3	3		ENSP00000408954.1
STEAP1B	ENST00000650428.1	n.159+24235C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.488 AC: 74090 AN: 151908 Hom.: 19948 Cov.: 32

Gnomad AFR AF: 0.327

Gnomad AMI AF: 0.712

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.446

Gnomad EAS AF: 0.0517

Gnomad SAS AF: 0.385

Gnomad FIN AF: 0.572

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.623

Gnomad OTH AF: 0.477

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

GnomAD4 genome AF: 0.488 AC: 74115 AN: 152026 Hom.: 19952 Cov.: 32 AF XY: 0.478 AC XY: 35535 AN XY: 74316

Gnomad4 AFR AF: 0.327

Gnomad4 AMR AF: 0.440

Gnomad4 ASJ AF: 0.446

Gnomad4 EAS AF: 0.0518

Gnomad4 SAS AF: 0.385

Gnomad4 FIN AF: 0.572

Gnomad4 NFE AF: 0.623

Gnomad4 OTH AF: 0.480

Alfa AF: 0.570 Hom.: 12189

Bravo AF: 0.467

Asia WGS AF: 0.253 AC: 881 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	0.46
DANN	Benign	0.70

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2905308; hg19: chr7-22648194;