rs13153333

Positions:

• chr5-91685570-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000651690.1(ENSG00000286121):​n.174-35469A>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 0.032 in 152,204 control chromosomes in the GnomAD database, including 93 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 0.032 (93 hom., cov: 32)
• Consequence: ENST00000651690.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.02

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.032 (4874/152204) while in subpopulation NFE AF= 0.0494 (3360/67964). AF 95% confidence interval is 0.048. There are 93 homozygotes in gnomad4. There are 2209 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 93 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000651690.1	n.174-35469A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0320 AC: 4873 AN: 152086 Hom.: 93 Cov.: 32

Gnomad AFR AF: 0.00939

Gnomad AMI AF: 0.0318

Gnomad AMR AF: 0.0263

Gnomad ASJ AF: 0.0429

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0143

Gnomad FIN AF: 0.0370

Gnomad MID AF: 0.0573

Gnomad NFE AF: 0.0494

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0320 AC: 4874 AN: 152204 Hom.: 93 Cov.: 32 AF XY: 0.0297 AC XY: 2209 AN XY: 74416

Gnomad4 AFR AF: 0.00936

Gnomad4 AMR AF: 0.0263

Gnomad4 ASJ AF: 0.0429

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0143

Gnomad4 FIN AF: 0.0370

Gnomad4 NFE AF: 0.0494

Gnomad4 OTH AF: 0.0303

Alfa AF: 0.0473 Hom.: 133

Bravo AF: 0.0312

Asia WGS AF: 0.0110 AC: 38 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	11
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: rs13153333; hg19: chr5-90981387;