7-22693350-G-T

Variant names:

• chr7-22693350-G-T
• rs2106549
• ENST00000915078.1:c.-145+13334C>A

Variant summary

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

The ENST00000915078.1(STEAP1B):​c.-145+13334C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.886 in 151,938 control chromosomes in the GnomAD database, including 60,839 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 0.89 (60839 hom., cov: 28)
• Consequence: STEAP1B ENST00000915078.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0490
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000915078.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STEAP1B	ENST00000915078.1		c.-145+13334C>A		intron	N/A	ENSP00000585137.1
	STEAP1B	ENST00000915079.1		c.-145+12277C>A		intron	N/A	ENSP00000585138.1
	STEAP1B	ENST00000915080.1		c.-104+12277C>A		intron	N/A	ENSP00000585139.1

Frequencies

GnomAD3 genomes AF: 0.886 AC: 134515 AN: 151822 Hom.: 60802 Cov.: 28

Gnomad AFR AF: 0.881

Gnomad AMI AF: 0.980

Gnomad AMR AF: 0.812

Gnomad ASJ AF: 0.917

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.942

Gnomad MID AF: 0.934

Gnomad NFE AF: 0.951

Gnomad OTH AF: 0.874

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

GnomAD4 genome AF: 0.886 AC: 134605 AN: 151938 Hom.: 60839 Cov.: 28 AF XY: 0.879 AC XY: 65261 AN XY: 74282

African (AFR) AF: 0.881 AC: 36477 AN: 41412

American (AMR) AF: 0.812 AC: 12369 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.917 AC: 3179 AN: 3468

East Asian (EAS) AF: 0.315 AC: 1620 AN: 5150

South Asian (SAS) AF: 0.690 AC: 3312 AN: 4800

European-Finnish (FIN) AF: 0.942 AC: 9963 AN: 10574

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.951 AC: 64680 AN: 67984

Other (OTH) AF: 0.873 AC: 1841 AN: 2110

Alfa AF: 0.920 Hom.: 31975

Bravo AF: 0.878

Asia WGS AF: 0.557 AC: 1943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.3
DANN	Benign	0.68
PhyloP100		0.049

Splicing

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

Other links and lift over

dbSNP: rs2106549; hg19: chr7-22732969;