rs7801617

Variant names:

• chr7-22718463-G-A
• rs7801617
• ENST00000650428.1:n.46+9105C>T

Your query was ambiguous. Multiple possible variants found:

• chr7-22718463-G-A
• chr7-22718463-G-C

Variant summary

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

The ENST00000650428.1(STEAP1B):​n.46+9105C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 152,118 control chromosomes in the GnomAD database, including 4,445 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 0.20 (4445 hom., cov: 32)
• Consequence: STEAP1B ENST00000650428.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.469
• Publications: 21 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=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.403 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650428.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	STEAP1B	ENST00000650428.1		n.46+9105C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.197 AC: 30017 AN: 152000 Hom.: 4443 Cov.: 32

Gnomad AFR AF: 0.408

Gnomad AMI AF: 0.148

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.00308

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.357

Gnomad NFE AF: 0.103

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.198 AC: 30052 AN: 152118 Hom.: 4445 Cov.: 32 AF XY: 0.198 AC XY: 14740 AN XY: 74370

African (AFR) AF: 0.408 AC: 16935 AN: 41486

American (AMR) AF: 0.148 AC: 2268 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 827 AN: 3462

East Asian (EAS) AF: 0.00309 AC: 16 AN: 5178

South Asian (SAS) AF: 0.144 AC: 694 AN: 4810

European-Finnish (FIN) AF: 0.158 AC: 1669 AN: 10588

Middle Eastern (MID) AF: 0.360 AC: 105 AN: 292

European-Non Finnish (NFE) AF: 0.103 AC: 7001 AN: 67998

Other (OTH) AF: 0.191 AC: 402 AN: 2110

Alfa AF: 0.141 Hom.: 4166

Bravo AF: 0.209

Asia WGS AF: 0.0870 AC: 302 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.9
DANN	Benign	0.58
PhyloP100		0.47

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7801617;

hg19: chr7-22758082;