12-98456417-C-T

Position:

• chr12-98456417-C-T

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC9A7P1	NR_033801.1	n.729G>A		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC9A7P1	ENST00000554295.1	n.729G>A		non_coding_transcript_exon_variant	1/1
SLC9A7P1	ENST00000556476.1	n.699G>A		non_coding_transcript_exon_variant	1/1

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

Gnomad4 AFR exome AF: 0.868

Gnomad4 AMR exome AF: 0.343

Gnomad4 ASJ exome AF: 0.581

Gnomad4 EAS exome AF: 0.466

Gnomad4 SAS exome AF: 0.528

Gnomad4 FIN exome AF: 0.495

Gnomad4 NFE exome AF: 0.595

Gnomad4 OTH exome AF: 0.586

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

Gnomad4 AFR AF: 0.840

Gnomad4 AMR AF: 0.456

Gnomad4 ASJ AF: 0.564

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.581

Alfa AF: 0.553 Hom.: 5932

Bravo AF: 0.614

Asia WGS AF: 0.486 AC: 1694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs829864; hg19: chr12-98850195;