7-22488971-C-T

Variant names:

• chr7-22488971-C-T
• rs10234308
• NM_001382447.1:c.762+3594G>A

Variant summary

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

The NM_001382447.1(STEAP1B):​c.762+3594G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0996 in 152,188 control chromosomes in the GnomAD database, including 869 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 0.10 (869 hom., cov: 32)
• Consequence: STEAP1B NM_001382447.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08
• 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.141 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
STEAP1B	NM_001382447.1	c.762+3594G>A		intron_variant	Intron 4 of 4	ENST00000678116.1	NP_001369376.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STEAP1B	ENST00000678116.1	c.762+3594G>A		intron_variant	Intron 4 of 4		NM_001382447.1	ENSP00000503251.1
STEAP1B	ENST00000404369.8	c.762+3594G>A		intron_variant	Intron 4 of 4	1		ENSP00000384370.4
STEAP1B	ENST00000406890.6	c.705+3594G>A		intron_variant	Intron 4 of 4	1		ENSP00000385239.2

Frequencies

GnomAD3 genomes AF: 0.0995 AC: 15132 AN: 152070 Hom.: 865 Cov.: 32

Gnomad AFR AF: 0.144

Gnomad AMI AF: 0.126

Gnomad AMR AF: 0.0559

Gnomad ASJ AF: 0.0651

Gnomad EAS AF: 0.000578

Gnomad SAS AF: 0.0298

Gnomad FIN AF: 0.126

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0925

Gnomad OTH AF: 0.0880

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

GnomAD4 genome AF: 0.0996 AC: 15158 AN: 152188 Hom.: 869 Cov.: 32 AF XY: 0.0989 AC XY: 7361 AN XY: 74406

African (AFR) AF: 0.144 AC: 5986 AN: 41506

American (AMR) AF: 0.0558 AC: 854 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0651 AC: 226 AN: 3470

East Asian (EAS) AF: 0.000579 AC: 3 AN: 5180

South Asian (SAS) AF: 0.0300 AC: 145 AN: 4826

European-Finnish (FIN) AF: 0.126 AC: 1332 AN: 10598

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0925 AC: 6291 AN: 68000

Other (OTH) AF: 0.0871 AC: 184 AN: 2112

Alfa AF: 0.0962 Hom.: 132

Bravo AF: 0.0977

Asia WGS AF: 0.0300 AC: 104 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.87
PhyloP100		-1.1
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10234308; hg19: chr7-22528590;