rs477687

Positions:

• chr5-135132010-G-A

Variant summary

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

The NR_161235.1(PITX1-AS1):​n.337-42032G>A 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 0.181 in 152,192 control chromosomes in the GnomAD database, including 2,702 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 0.18 (2702 hom., cov: 33)
• Consequence: PITX1-AS1 NR_161235.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.03

Genes affected

(HGNC:):

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=-0.29).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.247 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PITX1-AS1	NR_161235.1	n.337-42032G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000507058.1	n.47-1217G>A		intron_variant, non_coding_transcript_variant		3
PITX1-AS1	ENST00000624272.3	n.331-42032G>A		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27483 AN: 152074 Hom.: 2695 Cov.: 33

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.115

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.00520

Gnomad SAS AF: 0.0942

Gnomad FIN AF: 0.158

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.176

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

GnomAD4 genome AF: 0.181 AC: 27505 AN: 152192 Hom.: 2702 Cov.: 33 AF XY: 0.180 AC XY: 13367 AN XY: 74404

Gnomad4 AFR AF: 0.251

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.154

Gnomad4 EAS AF: 0.00521

Gnomad4 SAS AF: 0.0947

Gnomad4 FIN AF: 0.158

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.174

Alfa AF: 0.170 Hom.: 5316

Bravo AF: 0.182

Asia WGS AF: 0.0650 AC: 225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	17
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs477687; hg19: chr5-134467700;