5-135132010-G-A

Variant names:

• chr5-135132010-G-A
• rs477687
• ENST00000505828.5:n.281-42032G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000505828.5(PITX1-AS1):​n.281-42032G>A variant causes a intron 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 ENST00000505828.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.03
• Publications: 11 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

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.337-42032G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PITX1-AS1	ENST00000505828.5	TSL:4	n.281-42032G>A		intron	N/A
	PITX1-AS1	ENST00000507058.1	TSL:3	n.47-1217G>A		intron	N/A
	PITX1-AS1	ENST00000507641.5	TSL:3	n.430-15073G>A		intron	N/A

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

African (AFR) AF: 0.251 AC: 10437 AN: 41512

American (AMR) AF: 0.133 AC: 2033 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 533 AN: 3466

East Asian (EAS) AF: 0.00521 AC: 27 AN: 5180

South Asian (SAS) AF: 0.0947 AC: 457 AN: 4824

European-Finnish (FIN) AF: 0.158 AC: 1676 AN: 10600

Middle Eastern (MID) AF: 0.192 AC: 56 AN: 292

European-Non Finnish (NFE) AF: 0.174 AC: 11813 AN: 67992

Other (OTH) AF: 0.174 AC: 368 AN: 2114

Alfa AF: 0.173 Hom.: 8879

Bravo AF: 0.182

Asia WGS AF: 0.0650 AC: 225 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.29
CADD	Benign	17
DANN	Benign	0.72
PhyloP100		2.0

Splicing

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

Other links and lift over

dbSNP: rs477687; hg19: chr5-134467700;