chr5-135036995-T-C

Position:

• chr5-135036995-T-C

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+3455T>C 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 0.247 in 152,038 control chromosomes in the GnomAD database, including 5,159 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 0.25 (5159 hom., cov: 33)
• Consequence: PITX1-AS1 NR_161235.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229

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=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.456 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PITX1-AS1	NR_161235.1	n.267+3455T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PITX1-AS1	ENST00000624272.3	n.261+3455T>C		intron_variant, non_coding_transcript_variant		2
PITX1-AS1	ENST00000505828.5	n.99+3455T>C		intron_variant, non_coding_transcript_variant		4
PITX1-AS1	ENST00000507641.5	n.159+3455T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37551 AN: 151920 Hom.: 5157 Cov.: 33

Gnomad AFR AF: 0.168

Gnomad AMI AF: 0.358

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.472

Gnomad SAS AF: 0.416

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.247 AC: 37554 AN: 152038 Hom.: 5159 Cov.: 33 AF XY: 0.251 AC XY: 18623 AN XY: 74318

Gnomad4 AFR AF: 0.168

Gnomad4 AMR AF: 0.286

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.471

Gnomad4 SAS AF: 0.416

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.257

Gnomad4 OTH AF: 0.235

Alfa AF: 0.262 Hom.: 10288

Bravo AF: 0.243

Asia WGS AF: 0.460 AC: 1595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.1
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs31198; hg19: chr5-134372685;