chr5-4831488-T-C

Position:

• chr5-4831488-T-C

Variant summary

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

The ENST00000507435.1(ENSG00000248973):​n.207-25640A>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 0.239 in 151,976 control chromosomes in the GnomAD database, including 6,895 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 (6895 hom., cov: 32)
• Consequence: ENST00000507435.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.86

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107986400	XR_007059111.1	n.368-25640A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000507435.1	n.207-25640A>G		intron_variant, non_coding_transcript_variant		5
	ENST00000651493.1	n.369+10185A>G		intron_variant, non_coding_transcript_variant
	ENST00000651524.1	n.211+34528A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.239 AC: 36288 AN: 151858 Hom.: 6865 Cov.: 32

Gnomad AFR AF: 0.520

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.138

Gnomad EAS AF: 0.116

Gnomad SAS AF: 0.192

Gnomad FIN AF: 0.0784

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.239 AC: 36381 AN: 151976 Hom.: 6895 Cov.: 32 AF XY: 0.237 AC XY: 17571 AN XY: 74292

Gnomad4 AFR AF: 0.520

Gnomad4 AMR AF: 0.261

Gnomad4 ASJ AF: 0.138

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.191

Gnomad4 FIN AF: 0.0784

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.226

Alfa AF: 0.134 Hom.: 2507

Bravo AF: 0.266

Asia WGS AF: 0.210 AC: 731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.063
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs816475; hg19: chr5-4831601;