chr8-60938907-T-C

Variant names:

• chr8-60938907-T-C
• rs3748648
• ENST00000529239.1:n.965A>G

Variant summary

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

The ENST00000529239.1(NASPP1):​n.965A>G 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 0.356 in 1,576,514 control chromosomes in the GnomAD database, including 105,436 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 0.33 (8982 hom., cov: 32)
  • Exomes 𝑓: 0.36 (96454 hom.)
• Consequence: NASPP1 ENST00000529239.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.97

Genes affected

NASPP1 (HGNC:29910): (nuclear autoantigenic sperm protein pseudogene 1)

ENSG00000254777 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.48 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NASPP1		n.60938907T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NASPP1	ENST00000529239.1	n.965A>G		non_coding_transcript_exon_variant	Exon 1 of 1	6
ENSG00000254777	ENST00000526936.5	n.177-25823T>C		intron_variant	Intron 1 of 2	5
ENSG00000254777	ENST00000527672.1	n.323+18485T>C		intron_variant	Intron 2 of 4	2
ENSG00000254777	ENST00000529234.5	n.401-14023T>C		intron_variant	Intron 3 of 4	2

Frequencies

GnomAD3 genomes AF: 0.326 AC: 49614 AN: 151982 Hom.: 8986 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.367

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.378

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.377

Gnomad OTH AF: 0.360

GnomAD4 exome AF: 0.360 AC: 512145 AN: 1424414 Hom.: 96454 Cov.: 33 AF XY: 0.354 AC XY: 251667 AN XY: 710788

Gnomad4 AFR exome AF: 0.193

Gnomad4 AMR exome AF: 0.586

Gnomad4 ASJ exome AF: 0.353

Gnomad4 EAS exome AF: 0.227

Gnomad4 SAS exome AF: 0.172

Gnomad4 FIN exome AF: 0.374

Gnomad4 NFE exome AF: 0.375

Gnomad4 OTH exome AF: 0.350

GnomAD4 genome AF: 0.326 AC: 49630 AN: 152100 Hom.: 8982 Cov.: 32 AF XY: 0.326 AC XY: 24274 AN XY: 74350

Gnomad4 AFR AF: 0.196

Gnomad4 AMR AF: 0.490

Gnomad4 ASJ AF: 0.367

Gnomad4 EAS AF: 0.222

Gnomad4 SAS AF: 0.156

Gnomad4 FIN AF: 0.378

Gnomad4 NFE AF: 0.377

Gnomad4 OTH AF: 0.356

Alfa AF: 0.351 Hom.: 4497

Bravo AF: 0.338

Asia WGS AF: 0.180 AC: 626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	12
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3748648; hg19: chr8-61851466;