rs10064219

chr5-1384883-G-A

Variant summary

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

The ENST00000624349.1(ENSG00000279908):n.1527C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.164 in 152,230 control chromosomes in the GnomAD database, including 2,390 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 0.16 (2390 hom., cov: 33)
  • Exomes 𝑓: 0.20 (0 hom.)
• Consequence: ENST00000624349.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.354 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
	ENST00000624349.1	n.1527C>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24900 AN: 152102 Hom.: 2382 Cov.: 33

Gnomad AFR AF: 0.185

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.224

Gnomad ASJ AF: 0.219

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.287

Gnomad FIN AF: 0.112

Gnomad MID AF: 0.250

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.190

GnomAD4 exome AF: 0.200 AC: 2 AN: 10 Hom.: 0 Cov.: 0 AF XY: 0.200 AC XY: 2 AN XY: 10

Gnomad4 FIN exome AF: 0.500

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.250

GnomAD4 genome AF: 0.164 AC: 24931 AN: 152220 Hom.: 2390 Cov.: 33 AF XY: 0.169 AC XY: 12587 AN XY: 74426

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.224

Gnomad4 ASJ AF: 0.219

Gnomad4 EAS AF: 0.368

Gnomad4 SAS AF: 0.287

Gnomad4 FIN AF: 0.112

Gnomad4 NFE AF: 0.117

Gnomad4 OTH AF: 0.196

Alfa AF: 0.131 Hom.: 347

Bravo AF: 0.175

Asia WGS AF: 0.339 AC: 1181 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.8
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10064219; hg19: chr5-1384998; COSMIC: COSV72961788;