chr5-137859073-A-G

Variant names:

• chr5-137859073-A-G
• rs7722600
• ENST00000514616.7:n.561T>C

Variant summary

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

The ENST00000514616.7(PKD2L2-DT):​n.561T>C 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 0.179 in 152,198 control chromosomes in the GnomAD database, including 2,620 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 0.18 (2620 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: PKD2L2-DT ENST00000514616.7 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.13
• Publications: 16 publications found

Genes affected

PKD2L2-DT (HGNC:55557): (PKD2L2 divergent transcript)

NPY6R (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.204 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PKD2L2-DT	XR_007058950.1	n.3807T>C		non_coding_transcript_exon_variant	Exon 4 of 5
PKD2L2-DT	XR_948815.3	n.493T>C		non_coding_transcript_exon_variant	Exon 3 of 4
LOC107986368	XR_007058951.1	n.259-59A>G		intron_variant	Intron 3 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PKD2L2-DT	ENST00000514616.7	n.561T>C		non_coding_transcript_exon_variant	Exon 3 of 5	5
PKD2L2-DT	ENST00000661977.1	n.338T>C		non_coding_transcript_exon_variant	Exon 2 of 4
PKD2L2-DT	ENST00000666934.1	n.278T>C		non_coding_transcript_exon_variant	Exon 2 of 5

Frequencies

GnomAD3 genomes AF: 0.179 AC: 27217 AN: 152080 Hom.: 2617 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.185

Gnomad EAS AF: 0.0421

Gnomad SAS AF: 0.0859

Gnomad FIN AF: 0.218

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.168

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

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) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.179 AC: 27233 AN: 152198 Hom.: 2620 Cov.: 32 AF XY: 0.178 AC XY: 13231 AN XY: 74410

African (AFR) AF: 0.207 AC: 8613 AN: 41522

American (AMR) AF: 0.129 AC: 1978 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.185 AC: 640 AN: 3466

East Asian (EAS) AF: 0.0420 AC: 218 AN: 5190

South Asian (SAS) AF: 0.0856 AC: 413 AN: 4826

European-Finnish (FIN) AF: 0.218 AC: 2313 AN: 10588

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.185 AC: 12581 AN: 67994

Other (OTH) AF: 0.166 AC: 351 AN: 2114

Alfa AF: 0.176 Hom.: 7320

Bravo AF: 0.173

Asia WGS AF: 0.0760 AC: 265 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	12
DANN	Benign	0.84
PhyloP100		2.1

Splicing

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

Other links and lift over

dbSNP: rs7722600; hg19: chr5-137194762;