12-98456417-C-A

Variant names:

• chr12-98456417-C-A
• rs829864
• ENST00000554295.1:n.729G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000554295.1(SLC9A7P1):​n.729G>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SLC9A7P1 ENST00000554295.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.80
• Publications: 8 publications found

Genes affected

SLC9A7P1 (HGNC:):

SLC9A7P1 (HGNC:32679): (solute carrier family 9 member 7 pseudogene 1)

LINC02453 (HGNC:53392): (long intergenic non-protein coding RNA 2453)

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000554295.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC9A7P1	NR_033801.1		n.729G>T		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC9A7P1	ENST00000554295.1	TSL:6	n.729G>T		non_coding_transcript_exon	Exon 1 of 1
	SLC9A7P1	ENST00000556476.1	TSL:6	n.699G>T		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000302820	ENST00000789811.1		n.110+8906G>T		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 747846 Hom.: 0 Cov.: 10 AF XY: 0.00 AC XY: 0 AN XY: 398032

African (AFR) AF: 0.00 AC: 0 AN: 21402

American (AMR) AF: 0.00 AC: 0 AN: 40630

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 20444

East Asian (EAS) AF: 0.00 AC: 0 AN: 35896

South Asian (SAS) AF: 0.00 AC: 0 AN: 69170

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 51018

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 4312

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 468652

Other (OTH) AF: 0.00 AC: 0 AN: 36322

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 13835

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	3.5
DANN	Benign	0.71
PhyloP100		2.8

Splicing

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

Other links and lift over

dbSNP: rs829864; hg19: chr12-98850195;