rs2278335

Positions:

• chr8-10845943-G-A
• chr8-10845943-G-C

Variant summary

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

The NR_125432.1(PINX1-DT):​n.154-275G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.365 in 151,930 control chromosomes in the GnomAD database, including 11,175 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 0.37 (11175 hom., cov: 32)
• Consequence: PINX1-DT NR_125432.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.254

Genes affected

PINX1-DT (HGNC:55532): (PINX1 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.527 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PINX1-DT	NR_125432.1	n.154-275G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PINX1-DT	ENST00000655622.1	n.166-275G>A		intron_variant, non_coding_transcript_variant
PINX1-DT	ENST00000522026.2	n.156-275G>A		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55441 AN: 151812 Hom.: 11163 Cov.: 32

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.273

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.318

Gnomad OTH AF: 0.367

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.365 AC: 55487 AN: 151930 Hom.: 11175 Cov.: 32 AF XY: 0.359 AC XY: 26646 AN XY: 74266

Gnomad4 AFR AF: 0.533

Gnomad4 AMR AF: 0.273

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.221

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.318

Gnomad4 OTH AF: 0.370

Alfa AF: 0.315 Hom.: 1382

Bravo AF: 0.372

Asia WGS AF: 0.240 AC: 835 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.1
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2278335; hg19: chr8-10703453;