chr7-22709538-G-T

Variant names:

• chr7-22709538-G-T
• rs6949149
• ENST00000650428.1:n.46+18030C>A

Variant summary

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

The ENST00000650428.1(STEAP1B):​n.46+18030C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.122 in 152,224 control chromosomes in the GnomAD database, including 2,074 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 (2074 hom., cov: 33)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

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 (EAS) allele frequency at 95% confidence interval = 0.602 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	ENST00000650428.1	n.46+18030C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18552 AN: 152106 Hom.: 2066 Cov.: 33

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.0603

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.0934

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.311

Gnomad FIN AF: 0.0628

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0668

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.122 AC: 18593 AN: 152224 Hom.: 2074 Cov.: 33 AF XY: 0.128 AC XY: 9532 AN XY: 74420

Gnomad4 AFR AF: 0.120

Gnomad4 AMR AF: 0.196

Gnomad4 ASJ AF: 0.0934

Gnomad4 EAS AF: 0.620

Gnomad4 SAS AF: 0.311

Gnomad4 FIN AF: 0.0628

Gnomad4 NFE AF: 0.0668

Gnomad4 OTH AF: 0.140

Alfa AF: 0.0855 Hom.: 2045

Bravo AF: 0.129

Asia WGS AF: 0.422 AC: 1467 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	0.64
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6949149; hg19: chr7-22749157;