rs1989838

Positions:

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

Variant summary

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

The NR_122075.1(LOC401312):​n.1024+1534T>G 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 0.683 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: LOC401312 NR_122075.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.582

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

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC401312	NR_122075.1	n.1024+1534T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
STEAP1B	ENST00000414116.1	n.1024+1534T>G		intron_variant, non_coding_transcript_variant		1
STEAP1B	ENST00000442252.1	n.128+117T>G		intron_variant, non_coding_transcript_variant		1
STEAP1B	ENST00000649402.1	n.460+1534T>G		intron_variant, non_coding_transcript_variant
STEAP1B	ENST00000650428.1	n.47-28626T>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 NFE exome AF: 0.833

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

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.556

Gnomad4 EAS AF: 0.172

Gnomad4 SAS AF: 0.476

Gnomad4 FIN AF: 0.681

Gnomad4 NFE AF: 0.712

Gnomad4 OTH AF: 0.650

Alfa AF: 0.689 Hom.: 46193

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1989838; hg19: chr7-22701167;