5-132012478-A-G

Position:

• chr5-132012478-A-G

Variant summary

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

The ENST00000432558.1(ENSG00000231585):​n.99-211A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.782 in 152,152 control chromosomes in the GnomAD database, including 47,058 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 0.78 (47058 hom., cov: 32)
• Consequence: ENST00000432558.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.644

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.836 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124901062	XR_007058933.1	n.90+933A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000432558.1	n.99-211A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.782 AC: 118949 AN: 152032 Hom.: 47045 Cov.: 32

Gnomad AFR AF: 0.742

Gnomad AMI AF: 0.838

Gnomad AMR AF: 0.736

Gnomad ASJ AF: 0.745

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.782

Gnomad FIN AF: 0.797

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.842

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.782 AC: 119010 AN: 152152 Hom.: 47058 Cov.: 32 AF XY: 0.778 AC XY: 57842 AN XY: 74380

Gnomad4 AFR AF: 0.742

Gnomad4 AMR AF: 0.735

Gnomad4 ASJ AF: 0.745

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.782

Gnomad4 FIN AF: 0.797

Gnomad4 NFE AF: 0.842

Gnomad4 OTH AF: 0.788

Alfa AF: 0.810 Hom.: 10162

Bravo AF: 0.771

Asia WGS AF: 0.601 AC: 2090 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	9.5
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs246999; hg19: chr5-131348171;