rs4719711

Variant names:

• chr7-22716069-C-T
• rs4719711
• ENST00000650428.1:n.46+11499G>A

Variant summary

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

The ENST00000650428.1(STEAP1B):​n.46+11499G>A variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.104
• 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=-0.89).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STEAP1B	ENST00000650428.1	n.46+11499G>A		intron_variant	Intron 1 of 2

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

African (AFR) AF: 0.746 AC: 30959 AN: 41498

American (AMR) AF: 0.575 AC: 8799 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2184 AN: 3466

East Asian (EAS) AF: 0.242 AC: 1254 AN: 5178

South Asian (SAS) AF: 0.457 AC: 2205 AN: 4826

European-Finnish (FIN) AF: 0.441 AC: 4648 AN: 10544

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.519 AC: 35280 AN: 67924

Other (OTH) AF: 0.591 AC: 1250 AN: 2116

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
PhyloP100		-0.10

Splicing

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

Other links and lift over

dbSNP: rs4719711; hg19: chr7-22755688;