rs662204

chr5-41587588-G-A

Variant summary

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

The ENST00000504215.1(ENSG00000251478):n.200C>T variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.0917 in 688,522 control chromosomes in the GnomAD database, including 4,541 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 0.10 (966 hom., cov: 33)
  • Exomes 𝑓: 0.088 (3575 hom.)
• Consequence: ENST00000504215.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.50

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.65).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.174 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
	ENST00000504215.1	n.200C>T		non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15697 AN: 151998 Hom.: 964 Cov.: 33

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0451

Gnomad AMR AF: 0.0845

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.00407

Gnomad SAS AF: 0.0635

Gnomad FIN AF: 0.0507

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0802

Gnomad OTH AF: 0.111

GnomAD4 exome AF: 0.0884 AC: 47416 AN: 536406 Hom.: 3575 Cov.: 0 AF XY: 0.0877 AC XY: 25914 AN XY: 295470

Gnomad4 AFR exome AF: 0.196

Gnomad4 AMR exome AF: 0.0854

Gnomad4 ASJ exome AF: 0.136

Gnomad4 EAS exome AF: 0.00690

Gnomad4 SAS exome AF: 0.0780

Gnomad4 FIN exome AF: 0.0591

Gnomad4 NFE exome AF: 0.0922

Gnomad4 OTH exome AF: 0.102

GnomAD4 genome AF: 0.103 AC: 15700 AN: 152116 Hom.: 966 Cov.: 33 AF XY: 0.101 AC XY: 7479 AN XY: 74344

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.0843

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.00408

Gnomad4 SAS AF: 0.0627

Gnomad4 FIN AF: 0.0507

Gnomad4 NFE AF: 0.0803

Gnomad4 OTH AF: 0.109

Alfa AF: 0.100 Hom.: 111

Bravo AF: 0.110

Asia WGS AF: 0.0500 AC: 174 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.65
Cadd	Benign	5.9
Dann	Benign	0.26

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs662204; hg19: chr5-41587690;