8-60938907-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

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

ENSG00000254777 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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	ENST00000526936.6	n.177-25823T>C		intron_variant	Intron 1 of 3	5
ENSG00000254777	ENST00000527672.1	n.323+18485T>C		intron_variant	Intron 2 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

African (AFR) AF: 0.193 AC: 6284 AN: 32604

American (AMR) AF: 0.586 AC: 26137 AN: 44608

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 9127 AN: 25884

East Asian (EAS) AF: 0.227 AC: 8979 AN: 39540

South Asian (SAS) AF: 0.172 AC: 14701 AN: 85638

European-Finnish (FIN) AF: 0.374 AC: 19955 AN: 53380

Middle Eastern (MID) AF: 0.401 AC: 2284 AN: 5694

European-Non Finnish (NFE) AF: 0.375 AC: 403970 AN: 1077838

Other (OTH) AF: 0.350 AC: 20708 AN: 59228

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

African (AFR) AF: 0.196 AC: 8129 AN: 41520

American (AMR) AF: 0.490 AC: 7480 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.367 AC: 1273 AN: 3472

East Asian (EAS) AF: 0.222 AC: 1151 AN: 5182

South Asian (SAS) AF: 0.156 AC: 753 AN: 4826

European-Finnish (FIN) AF: 0.378 AC: 3987 AN: 10556

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.377 AC: 25650 AN: 67948

Other (OTH) AF: 0.356 AC: 752 AN: 2114

Alfa AF: 0.352 Hom.: 6275

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
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs3748648; hg19: chr8-61851466;