5-135036995-T-C

Variant names:

• chr5-135036995-T-C
• rs31198
• ENST00000505828.5:n.99+3455T>C

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+3455T>C variant causes a intron 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 ENST00000505828.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229
• Publications: 36 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=-0.83).
• 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 rank	MANE	Protein	UniProt
PITX1-AS1	NR_161235.1	n.267+3455T>C		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+3455T>C		intron_variant	Intron 1 of 4	4
PITX1-AS1	ENST00000507641.5	n.159+3455T>C		intron_variant	Intron 1 of 4	3
PITX1-AS1	ENST00000624272.3	n.261+3455T>C		intron_variant	Intron 1 of 5	2
PITX1-AS1	ENST00000806983.1	n.119+3455T>C		intron_variant	Intron 1 of 4

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

African (AFR) AF: 0.168 AC: 6962 AN: 41492

American (AMR) AF: 0.286 AC: 4369 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 808 AN: 3472

East Asian (EAS) AF: 0.471 AC: 2431 AN: 5158

South Asian (SAS) AF: 0.416 AC: 1996 AN: 4802

European-Finnish (FIN) AF: 0.251 AC: 2654 AN: 10570

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17449 AN: 67950

Other (OTH) AF: 0.235 AC: 497 AN: 2112

Alfa AF: 0.257 Hom.: 16652

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
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs31198; hg19: chr5-134372685;