rs4331913

Positions:

• chr5-29246702-C-T

Variant summary

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

The ENST00000651494.1(ENSG00000286182):​n.172-4714G>A 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 0.424 in 151,662 control chromosomes in the GnomAD database, including 14,043 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 0.42 (14043 hom., cov: 32)
• Consequence: ENST00000651494.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.722

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.495 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651494.1	n.172-4714G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64354 AN: 151544 Hom.: 14043 Cov.: 32

Gnomad AFR AF: 0.501

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.378

Gnomad EAS AF: 0.258

Gnomad SAS AF: 0.432

Gnomad FIN AF: 0.315

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.454

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

GnomAD4 genome AF: 0.424 AC: 64376 AN: 151662 Hom.: 14043 Cov.: 32 AF XY: 0.421 AC XY: 31205 AN XY: 74102

Gnomad4 AFR AF: 0.501

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.378

Gnomad4 EAS AF: 0.259

Gnomad4 SAS AF: 0.429

Gnomad4 FIN AF: 0.315

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.457

Alfa AF: 0.418 Hom.: 18372

Bravo AF: 0.434

Asia WGS AF: 0.389 AC: 1353 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.89
DANN	Benign	0.10

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4331913; hg19: chr5-29246809;