12-98456417-C-T

Variant names:

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

Variant summary

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

The NR_033801.1(SLC9A7P1):​n.729G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.575 in 899,738 control chromosomes in the GnomAD database, including 155,323 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 0.61 (29676 hom., cov: 32)
  • Exomes 𝑓: 0.57 (125647 hom.)
• Consequence: SLC9A7P1 NR_033801.1 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.66).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.833 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_033801.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.606 AC: 92023 AN: 151928 Hom.: 29624 Cov.: 32

Gnomad AFR AF: 0.840

Gnomad AMI AF: 0.664

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.564

Gnomad EAS AF: 0.438

Gnomad SAS AF: 0.524

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.580

GnomAD4 exome AF: 0.569 AC: 425503 AN: 747694 Hom.: 125647 Cov.: 10 AF XY: 0.567 AC XY: 225561 AN XY: 397944

African (AFR) AF: 0.868 AC: 18579 AN: 21400

American (AMR) AF: 0.343 AC: 13917 AN: 40614

Ashkenazi Jewish (ASJ) AF: 0.581 AC: 11886 AN: 20442

East Asian (EAS) AF: 0.466 AC: 16713 AN: 35896

South Asian (SAS) AF: 0.528 AC: 36500 AN: 69158

European-Finnish (FIN) AF: 0.495 AC: 25243 AN: 51016

Middle Eastern (MID) AF: 0.621 AC: 2678 AN: 4312

European-Non Finnish (NFE) AF: 0.595 AC: 278696 AN: 468540

Other (OTH) AF: 0.586 AC: 21291 AN: 36316

GnomAD4 genome AF: 0.606 AC: 92126 AN: 152044 Hom.: 29676 Cov.: 32 AF XY: 0.599 AC XY: 44522 AN XY: 74324

African (AFR) AF: 0.840 AC: 34879 AN: 41500

American (AMR) AF: 0.456 AC: 6957 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.564 AC: 1952 AN: 3462

East Asian (EAS) AF: 0.438 AC: 2253 AN: 5148

South Asian (SAS) AF: 0.522 AC: 2519 AN: 4828

European-Finnish (FIN) AF: 0.481 AC: 5079 AN: 10562

Middle Eastern (MID) AF: 0.619 AC: 182 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36474 AN: 67968

Other (OTH) AF: 0.581 AC: 1225 AN: 2108

Alfa AF: 0.561 Hom.: 13835

Bravo AF: 0.614

Asia WGS AF: 0.486 AC: 1694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.66
CADD	Benign	4.2
DANN	Benign	0.74
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;