7-22715149-G-T

Position:

• chr7-22715149-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+12419C>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 0.777 in 152,124 control chromosomes in the GnomAD database, including 47,241 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 0.78 (47241 hom., cov: 31)
• Consequence: STEAP1B ENST00000650428.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.13

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=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
STEAP1B	ENST00000650428.1	n.46+12419C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.776 AC: 118026 AN: 152004 Hom.: 47169 Cov.: 31

Gnomad AFR AF: 0.940

Gnomad AMI AF: 0.699

Gnomad AMR AF: 0.836

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.613

Gnomad MID AF: 0.801

Gnomad NFE AF: 0.666

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.777 AC: 118159 AN: 152124 Hom.: 47241 Cov.: 31 AF XY: 0.780 AC XY: 57985 AN XY: 74378

Gnomad4 AFR AF: 0.940

Gnomad4 AMR AF: 0.836

Gnomad4 ASJ AF: 0.786

Gnomad4 EAS AF: 0.999

Gnomad4 SAS AF: 0.858

Gnomad4 FIN AF: 0.613

Gnomad4 NFE AF: 0.666

Gnomad4 OTH AF: 0.805

Alfa AF: 0.682 Hom.: 18387

Bravo AF: 0.802

Asia WGS AF: 0.930 AC: 3232 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.034
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7776857; hg19: chr7-22754768;