rs7744601

Positions:

• chr6-7988677-T-C
• chr6-7988677-T-G

Variant summary

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

The NR_027712.1(PIP5K1P1):​n.2576T>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 0.239 in 151,742 control chromosomes in the GnomAD database, including 5,294 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 0.24 (5294 hom., cov: 31)
• Consequence: PIP5K1P1 NR_027712.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.323

Genes affected

PIP5K1P1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.405 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PIP5K1P1	NR_027712.1	n.2576T>C		non_coding_transcript_exon_variant	1/1
BLOC1S5-TXNDC5	NR_037616.1	n.422+37690A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36180 AN: 151636 Hom.: 5285 Cov.: 31

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.435

Gnomad AMR AF: 0.217

Gnomad ASJ AF: 0.146

Gnomad EAS AF: 0.0766

Gnomad SAS AF: 0.140

Gnomad FIN AF: 0.135

Gnomad MID AF: 0.166

Gnomad NFE AF: 0.178

Gnomad OTH AF: 0.224

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

GnomAD4 genome AF: 0.239 AC: 36239 AN: 151742 Hom.: 5294 Cov.: 31 AF XY: 0.234 AC XY: 17366 AN XY: 74144

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.218

Gnomad4 ASJ AF: 0.146

Gnomad4 EAS AF: 0.0766

Gnomad4 SAS AF: 0.140

Gnomad4 FIN AF: 0.135

Gnomad4 NFE AF: 0.178

Gnomad4 OTH AF: 0.226

Alfa AF: 0.0866 Hom.: 114

Bravo AF: 0.255

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	14
DANN	Benign	0.80

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7744601; hg19: chr6-7988910;