rs4719711

Positions:

• chr7-22716069-C-T

Variant summary

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

The ENST00000650428.1(STEAP1B):​n.46+11499G>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 0.574 in 152,050 control chromosomes in the GnomAD database, including 26,172 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 0.57 (26172 hom., cov: 32)
• Consequence: STEAP1B ENST00000650428.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104

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 (AFR) allele frequency at 95% confidence interval = 0.739 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+11499G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87190 AN: 151932 Hom.: 26154 Cov.: 32

Gnomad AFR AF: 0.746

Gnomad AMI AF: 0.516

Gnomad AMR AF: 0.575

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.242

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.441

Gnomad MID AF: 0.725

Gnomad NFE AF: 0.519

Gnomad OTH AF: 0.591

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

GnomAD4 genome AF: 0.574 AC: 87263 AN: 152050 Hom.: 26172 Cov.: 32 AF XY: 0.569 AC XY: 42308 AN XY: 74306

Gnomad4 AFR AF: 0.746

Gnomad4 AMR AF: 0.575

Gnomad4 ASJ AF: 0.630

Gnomad4 EAS AF: 0.242

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.441

Gnomad4 NFE AF: 0.519

Gnomad4 OTH AF: 0.591

Alfa AF: 0.543 Hom.: 3919

Bravo AF: 0.595

Asia WGS AF: 0.385 AC: 1337 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	1.6
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4719711; hg19: chr7-22755688;