chr5-135036180-G-T

Variant names:

• chr5-135036180-G-T
• rs39882
• ENST00000505828.5:n.99+2640G>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000505828.5(PITX1-AS1):​n.99+2640G>T variant causes a intron 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 ENST00000505828.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850
• Publications: 4 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PITX1-AS1	NR_161235.1	n.267+2640G>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PITX1-AS1	ENST00000505828.5	n.99+2640G>T		intron_variant	Intron 1 of 4	4
PITX1-AS1	ENST00000507641.5	n.159+2640G>T		intron_variant	Intron 1 of 4	3
PITX1-AS1	ENST00000624272.3	n.261+2640G>T		intron_variant	Intron 1 of 5	2
PITX1-AS1	ENST00000806983.1	n.119+2640G>T		intron_variant	Intron 1 of 4

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

African (AFR) AF: 0.755 AC: 31305 AN: 41444

American (AMR) AF: 0.510 AC: 7779 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.298 AC: 1035 AN: 3470

East Asian (EAS) AF: 0.475 AC: 2447 AN: 5152

South Asian (SAS) AF: 0.467 AC: 2245 AN: 4808

European-Finnish (FIN) AF: 0.328 AC: 3453 AN: 10534

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.372 AC: 25288 AN: 67894

Other (OTH) AF: 0.457 AC: 966 AN: 2112

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
PhyloP100		-0.085

Splicing

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

Other links and lift over

dbSNP: rs39882; hg19: chr5-134371870;