chr5-135141069-C-A

Variant names:

• chr5-135141069-C-A
• rs17716310
• ENST00000505828.5:n.281-32973C>A

Variant summary

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

The ENST00000505828.5(PITX1-AS1):​n.281-32973C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.306 in 151,976 control chromosomes in the GnomAD database, including 7,912 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 (7912 hom., cov: 32)
• Consequence: PITX1-AS1 ENST00000505828.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.554
• Publications: 5 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.627 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000505828.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PITX1-AS1	NR_161235.1		n.337-32973C>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PITX1-AS1	ENST00000505828.5	TSL:4	n.281-32973C>A		intron	N/A
	PITX1-AS1	ENST00000507641.5	TSL:3	n.430-6014C>A		intron	N/A
	PITX1-AS1	ENST00000513931.2	TSL:3	n.209+12706C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.306 AC: 46491 AN: 151858 Hom.: 7909 Cov.: 32

Gnomad AFR AF: 0.173

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.313

Gnomad ASJ AF: 0.360

Gnomad EAS AF: 0.646

Gnomad SAS AF: 0.365

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.348

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.306 AC: 46520 AN: 151976 Hom.: 7912 Cov.: 32 AF XY: 0.306 AC XY: 22732 AN XY: 74264

African (AFR) AF: 0.174 AC: 7213 AN: 41484

American (AMR) AF: 0.313 AC: 4785 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.360 AC: 1250 AN: 3468

East Asian (EAS) AF: 0.646 AC: 3318 AN: 5140

South Asian (SAS) AF: 0.366 AC: 1759 AN: 4808

European-Finnish (FIN) AF: 0.339 AC: 3569 AN: 10540

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.348 AC: 23652 AN: 67942

Other (OTH) AF: 0.308 AC: 649 AN: 2110

Alfa AF: 0.314 Hom.: 3790

Bravo AF: 0.301

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.93
DANN	Benign	0.51
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs17716310; hg19: chr5-134476759; COSMIC: COSV71405646;