rs17716310

Positions:

• chr5-135141069-C-A
• chr5-135141069-C-T

Variant summary

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

The ENST00000624272.3(PITX1-AS1):​n.331-32973C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 151,976 control chromosomes in the GnomAD database, including 7,912 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 0.31 (7912 hom., cov: 32)
• Consequence: PITX1-AS1 ENST00000624272.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554

Genes affected

PITX1-AS1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PITX1-AS1	NR_161235.1	n.337-32973C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PITX1-AS1	ENST00000505828.5	n.281-32973C>A		intron_variant		4
PITX1-AS1	ENST00000507641.5	n.430-6014C>A		intron_variant		3
PITX1-AS1	ENST00000513931.2	n.209+12706C>A		intron_variant		3
PITX1-AS1	ENST00000624272.3	n.331-32973C>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46491 AN: 151858 Hom.: 7909 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.306 AC: 46520 AN: 151976 Hom.: 7912 Cov.: 32 AF XY: 0.306 AC XY: 22732 AN XY: 74264

Gnomad4 AFR AF: 0.174

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.360

Gnomad4 EAS AF: 0.646

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.348

Gnomad4 OTH AF: 0.308

Alfa AF: 0.286 Hom.: 1957

Bravo AF: 0.301

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.93
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17716310; hg19: chr5-134476759; COSMIC: COSV71405646;