rs78958330

chr2-91893583-T-C

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000398120.6(SLC9B1P2):n.449-95A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. 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 0.000040 (0 hom., cov: 33)
  • Exomes 𝑓: 0.00049 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC9B1P2 ENST00000398120.6 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.902

Genes affected

SLC9B1P2 (HGNC:37493): (solute carrier family 9 member B1 pseudogene 2)

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC9B1P2	ENST00000398120.6	n.449-95A>G		intron_variant, non_coding_transcript_variant
	ENST00000606405.1	n.168-95A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.00 AC: 6 AN: 148530 Hom.: 0 Cov.: 33 FAILED QC

Gnomad AFR AF: 0.0000493

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000680

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.000199

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000100

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.000492

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000490 AC: 158 AN: 322544 Hom.: 0 AF XY: 0.000410 AC XY: 72 AN XY: 175552

Gnomad4 AFR exome AF: 0.00108

Gnomad4 AMR exome AF: 0.000670

Gnomad4 ASJ exome AF: 0.000642

Gnomad4 EAS exome AF: 0.000653

Gnomad4 SAS exome AF: 0.000407

Gnomad4 FIN exome AF: 0.000206

Gnomad4 NFE exome AF: 0.000477

Gnomad4 OTH exome AF: 0.000329

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000404 AC: 6 AN: 148630 Hom.: 0 Cov.: 33 AF XY: 0.0000690 AC XY: 5 AN XY: 72476

Gnomad4 AFR AF: 0.0000492

Gnomad4 AMR AF: 0.0000679

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.000200

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000100

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.000486

Alfa AF: 0.0158 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.70
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs78958330; hg19: chr2-92081609;