5-1624236-C-T

Position:

• chr5-1624236-C-T

Variant summary

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

The ENST00000507290.5(ENSG00000291079):​n.437+8408G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.344 in 145,666 control chromosomes in the GnomAD database, including 9,024 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 0.34 (9024 hom., cov: 29)
• Consequence: ENSG00000291079 ENST00000507290.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24

Genes affected

ENSG00000291079 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.409 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PDCD6P1	NR_003713.1	n.260+8609G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000291079	ENST00000507290.5	n.437+8408G>A		intron_variant		1
ENSG00000291079	ENST00000507505.5	n.257+8609G>A		intron_variant		1
ENSG00000291079	ENST00000507841.5	n.1385+2550G>A		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.344 AC: 50116 AN: 145532 Hom.: 9014 Cov.: 29

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.416

Gnomad ASJ AF: 0.214

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.502

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.344 AC: 50155 AN: 145666 Hom.: 9024 Cov.: 29 AF XY: 0.348 AC XY: 24795 AN XY: 71180

Gnomad4 AFR AF: 0.222

Gnomad4 AMR AF: 0.417

Gnomad4 ASJ AF: 0.214

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.348

Gnomad4 FIN AF: 0.502

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.330

Alfa AF: 0.353 Hom.: 19745

Bravo AF: 0.320

Asia WGS AF: 0.300 AC: 1043 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.45
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1968011; hg19: chr5-1624351;