5-135329392-G-T

Position:

• chr5-135329392-G-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NR_161235.1(PITX1-AS1):​n.468-4366G>T 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 0.314 in 152,180 control chromosomes in the GnomAD database, including 10,580 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 (10580 hom., cov: 33)
• Consequence: PITX1-AS1 NR_161235.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.636

Genes affected

PITX1-AS1 (HGNC:48332): (PITX1 antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.623 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PITX1-AS1	NR_161235.1	n.468-4366G>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PITX1-AS1	ENST00000624272.3	n.462-4366G>T		intron_variant, non_coding_transcript_variant		2
PITX1-AS1	ENST00000513931.2	n.436-8543G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47620 AN: 152062 Hom.: 10526 Cov.: 33

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.153

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.141

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.304

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

GnomAD4 genome AF: 0.314 AC: 47734 AN: 152180 Hom.: 10580 Cov.: 33 AF XY: 0.308 AC XY: 22893 AN XY: 74396

Gnomad4 AFR AF: 0.629

Gnomad4 AMR AF: 0.254

Gnomad4 ASJ AF: 0.246

Gnomad4 EAS AF: 0.153

Gnomad4 SAS AF: 0.203

Gnomad4 FIN AF: 0.141

Gnomad4 NFE AF: 0.186

Gnomad4 OTH AF: 0.301

Alfa AF: 0.203 Hom.: 5247

Bravo AF: 0.337

Asia WGS AF: 0.214 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
CADD	Benign	9.7
DANN	Benign	0.87

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13163460; hg19: chr5-134665082;