7-22709538-G-T

Position:

• chr7-22709538-G-T

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, non coding transcript 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, non_coding_transcript
• 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STEAP1B	ENST00000650428.1	n.46+18030C>A		intron_variant, non_coding_transcript_variant

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;