chr5-33121891-C-G

Position:

• chr5-33121891-C-G

Variant summary

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

The ENST00000657441.1(ENSG00000250697):​n.270-98564G>C 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 0.555 in 152,092 control chromosomes in the GnomAD database, including 24,697 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 0.55 (24697 hom., cov: 32)
• Consequence: ENST00000657441.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.217

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.745 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
	ENST00000657441.1	n.270-98564G>C		intron_variant, non_coding_transcript_variant
	ENST00000510327.2	n.503-98564G>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84270 AN: 151974 Hom.: 24646 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.519

Gnomad AMR AF: 0.480

Gnomad ASJ AF: 0.495

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.452

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.480

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.555 AC: 84381 AN: 152092 Hom.: 24697 Cov.: 32 AF XY: 0.551 AC XY: 40927 AN XY: 74330

Gnomad4 AFR AF: 0.752

Gnomad4 AMR AF: 0.480

Gnomad4 ASJ AF: 0.495

Gnomad4 EAS AF: 0.527

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.452

Gnomad4 NFE AF: 0.480

Gnomad4 OTH AF: 0.541

Alfa AF: 0.518 Hom.: 2616

Bravo AF: 0.568

Asia WGS AF: 0.499 AC: 1737 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.3
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1981968; hg19: chr5-33121997;