7-77671409-C-T

Variant names:

• chr7-77671409-C-T
• rs12537271
• ENST00000440088.5:n.371-12091G>A

Variant summary

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

The ENST00000440088.5(APTR):​n.371-12091G>A variant causes a intron 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 ENST00000440088.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114
• Publications: 12 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000440088.5. 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
	APTR	NR_134251.1		n.222-10076G>A		intron	N/A
	APTR	NR_134253.1		n.498-12091G>A		intron	N/A
	APTR	NR_134254.1		n.371-12091G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	APTR	ENST00000440088.5	TSL:1	n.371-12091G>A		intron	N/A
	APTR	ENST00000430801.6	TSL:5	n.222-10076G>A		intron	N/A
	APTR	ENST00000659053.1		n.488-10076G>A		intron	N/A

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

African (AFR) AF: 0.478 AC: 19733 AN: 41246

American (AMR) AF: 0.313 AC: 4756 AN: 15176

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 1137 AN: 3468

East Asian (EAS) AF: 0.134 AC: 692 AN: 5162

South Asian (SAS) AF: 0.334 AC: 1603 AN: 4800

European-Finnish (FIN) AF: 0.286 AC: 2996 AN: 10468

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.321 AC: 21811 AN: 67926

Other (OTH) AF: 0.340 AC: 716 AN: 2104

Alfa AF: 0.338 Hom.: 1484

Bravo AF: 0.361

Asia WGS AF: 0.261 AC: 911 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.2
DANN	Benign	0.40
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs12537271; hg19: chr7-77300726;