rs1989838

Variant names:

• chr7-22661548-A-C
• rs1989838
• ENST00000414116.1:n.1024+1534T>G

Your query was ambiguous. Multiple possible variants found:

• chr7-22661548-A-C
• chr7-22661548-A-T

Variant summary

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

The ENST00000414116.1(STEAP1B):​n.1024+1534T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 152,104 control chromosomes in the GnomAD database, including 36,514 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 0.68 (36512 hom., cov: 32)
  • Exomes 𝑓: 0.83 (2 hom.)
• Consequence: STEAP1B ENST00000414116.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582
• Publications: 9 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]

LOC401312 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.72 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC401312	NR_122075.1	n.1024+1534T>G		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
STEAP1B	ENST00000414116.1	n.1024+1534T>G		intron_variant	Intron 2 of 4	1
STEAP1B	ENST00000442252.1	n.128+117T>G		intron_variant	Intron 1 of 1	1
STEAP1B	ENST00000649402.1	n.460+1534T>G		intron_variant	Intron 4 of 7
STEAP1B	ENST00000650428.1	n.47-28626T>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.683 AC: 103839 AN: 151980 Hom.: 36468 Cov.: 32

Gnomad AFR AF: 0.726

Gnomad AMI AF: 0.727

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.556

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.477

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.649

GnomAD4 exome AF: 0.833 AC: 5 AN: 6 Hom.: 2 AF XY: 0.750 AC XY: 3 AN XY: 4

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.833 AC: 5 AN: 6

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.683 AC: 103951 AN: 152098 Hom.: 36512 Cov.: 32 AF XY: 0.675 AC XY: 50209 AN XY: 74356

African (AFR) AF: 0.727 AC: 30141 AN: 41486

American (AMR) AF: 0.713 AC: 10893 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.556 AC: 1929 AN: 3472

East Asian (EAS) AF: 0.172 AC: 889 AN: 5156

South Asian (SAS) AF: 0.476 AC: 2293 AN: 4816

European-Finnish (FIN) AF: 0.681 AC: 7214 AN: 10592

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.712 AC: 48382 AN: 67978

Other (OTH) AF: 0.650 AC: 1373 AN: 2112

Alfa AF: 0.692 Hom.: 59701

Bravo AF: 0.688

Asia WGS AF: 0.386 AC: 1346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.68
PhyloP100		-0.58

Splicing

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

Other links and lift over

dbSNP: rs1989838; hg19: chr7-22701167;