7-77671409-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_134251.1(APTR):n.222-10076G>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 0.355 in 151,554 control chromosomes in the GnomAD database, including 10,130 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 0.36 (10130 hom., cov: 28)
• Consequence: APTR NR_134251.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114

Genes affected

APTR (HGNC:44173): (Alu-mediated CDKN1A/p21 transcriptional regulator)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.473 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
APTR	NR_134251.1	n.222-10076G>A		intron_variant, non_coding_transcript_variant
APTR	NR_134253.1	n.498-12091G>A		intron_variant, non_coding_transcript_variant
APTR	NR_134254.1	n.371-12091G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
APTR	ENST00000440088.5	n.371-12091G>A		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53743 AN: 151436 Hom.: 10105 Cov.: 28

Gnomad AFR AF: 0.478

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.314

Gnomad ASJ AF: 0.328

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.333

Gnomad FIN AF: 0.286

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.321

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.355 AC: 53826 AN: 151554 Hom.: 10130 Cov.: 28 AF XY: 0.350 AC XY: 25935 AN XY: 74030

Gnomad4 AFR AF: 0.478

Gnomad4 AMR AF: 0.313

Gnomad4 ASJ AF: 0.328

Gnomad4 EAS AF: 0.134

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.286

Gnomad4 NFE AF: 0.321

Gnomad4 OTH AF: 0.340

Alfa AF: 0.333 Hom.: 1391

Bravo AF: 0.361

Asia WGS AF: 0.261 AC: 911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	4.2
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12537271; hg19: chr7-77300726;