5-135036180-G-T

Position:

• chr5-135036180-G-T

Variant summary

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

The NR_161235.1(PITX1-AS1):​n.267+2640G>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 0.494 in 151,874 control chromosomes in the GnomAD database, including 20,853 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 0.49 (20853 hom., cov: 31)
• Consequence: PITX1-AS1 NR_161235.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.748 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PITX1-AS1	NR_161235.1	n.267+2640G>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.261+2640G>T		intron_variant, non_coding_transcript_variant		2
PITX1-AS1	ENST00000505828.5	n.99+2640G>T		intron_variant, non_coding_transcript_variant		4
PITX1-AS1	ENST00000507641.5	n.159+2640G>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.493 AC: 74817 AN: 151756 Hom.: 20786 Cov.: 31

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.383

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.298

Gnomad EAS AF: 0.476

Gnomad SAS AF: 0.466

Gnomad FIN AF: 0.328

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.494 AC: 74953 AN: 151874 Hom.: 20853 Cov.: 31 AF XY: 0.489 AC XY: 36281 AN XY: 74216

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.510

Gnomad4 ASJ AF: 0.298

Gnomad4 EAS AF: 0.475

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.328

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.457

Alfa AF: 0.320 Hom.: 1434

Bravo AF: 0.517

Asia WGS AF: 0.525 AC: 1822 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.8
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs39882; hg19: chr5-134371870;