rs6752260

Variant names:

• chr2-64522449-G-A
• rs6752260
• ENST00000561559.3:n.2337C>T

Your query was ambiguous. Multiple possible variants found:

• chr2-64522449-G-A
• chr2-64522449-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

Genes affected

AFTPH-DT (HGNC:52788): (AFTPH divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_136167.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AFTPH-DT	NR_136167.1		n.1707C>T		non_coding_transcript_exon	Exon 1 of 1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	AFTPH-DT	ENST00000561559.3	TSL:6	n.2337C>T		non_coding_transcript_exon	Exon 1 of 1
	AFTPH-DT	ENST00000789328.1		n.1901C>T		non_coding_transcript_exon	Exon 2 of 2

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.691 AC: 28615 AN: 41422

American (AMR) AF: 0.321 AC: 4902 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.362 AC: 1256 AN: 3472

East Asian (EAS) AF: 0.463 AC: 2398 AN: 5184

South Asian (SAS) AF: 0.467 AC: 2251 AN: 4818

European-Finnish (FIN) AF: 0.260 AC: 2739 AN: 10540

Middle Eastern (MID) AF: 0.344 AC: 101 AN: 294

European-Non Finnish (NFE) AF: 0.315 AC: 21375 AN: 67946

Other (OTH) AF: 0.417 AC: 878 AN: 2106

Alfa AF: 0.364 Hom.: 4327

Bravo AF: 0.438

Asia WGS AF: 0.460 AC: 1594 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.9
DANN	Benign	0.60
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs6752260; hg19: chr2-64749583;