rs6752260

Positions:

• chr2-64522449-G-A

Variant summary

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

The NR_136167.1(AFTPH-DT):​n.1707C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 151,962 control chromosomes in the GnomAD database, including 15,986 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 0.43 (15986 hom., cov: 32)
  • Failed GnomAD Quality Control
• Consequence: AFTPH-DT NR_136167.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.21

Genes affected

AFTPH-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
AFTPH-DT	NR_136167.1	n.1707C>T		non_coding_transcript_exon_variant	1/1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
AFTPH-DT	ENST00000561559.2	n.1662C>T		non_coding_transcript_exon_variant	1/1	6

Frequencies

GnomAD3 genomes AF: 0.427 AC: 64776 AN: 151842 Hom.: 15954 Cov.: 32

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.321

Gnomad ASJ AF: 0.362

Gnomad EAS AF: 0.462

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.260

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.315

Gnomad OTH AF: 0.420

GnomAD4 exome Data not reliable, filtered out with message: AC0 AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

GnomAD4 genome AF: 0.427 AC: 64863 AN: 151962 Hom.: 15986 Cov.: 32 AF XY: 0.426 AC XY: 31670 AN XY: 74286

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.321

Gnomad4 ASJ AF: 0.362

Gnomad4 EAS AF: 0.463

Gnomad4 SAS AF: 0.467

Gnomad4 FIN AF: 0.260

Gnomad4 NFE AF: 0.315

Gnomad4 OTH AF: 0.417

Alfa AF: 0.353 Hom.: 3241

Bravo AF: 0.438

Asia WGS AF: 0.460 AC: 1594 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.9
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6752260; hg19: chr2-64749583;