5-1891707-A-G

Position:

• chr5-1891707-A-G

Variant summary

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

The ENST00000514569.1(CTD-2194D22.4):​n.108+3425A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.479 in 151,890 control chromosomes in the GnomAD database, including 17,521 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 0.48 (17521 hom., cov: 33)
• Consequence: CTD-2194D22.4 ENST00000514569.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95

Genes affected

CTD-2194D22.4 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.508 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CTD-2194D22.4	NR_109912.1	n.109+3425A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CTD-2194D22.4	ENST00000514569.1	n.108+3425A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.479 AC: 72658 AN: 151772 Hom.: 17503 Cov.: 33

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.427

Gnomad AMR AF: 0.518

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.516

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.476

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.479 AC: 72722 AN: 151890 Hom.: 17521 Cov.: 33 AF XY: 0.484 AC XY: 35917 AN XY: 74230

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.518

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.515

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.476

Gnomad4 OTH AF: 0.493

Alfa AF: 0.480 Hom.: 6874

Bravo AF: 0.476

Asia WGS AF: 0.467 AC: 1623 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.076
DANN	Benign	0.21

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10866528; hg19: chr5-1891821;