rs2038024

Positions:

• chr1-169486744-C-A

Variant summary

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

The ENST00000392097.5(ENSG00000213062):​n.669C>A 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 0.873 in 152,210 control chromosomes in the GnomAD database, including 58,201 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 0.87 (58198 hom., cov: 32)
  • Exomes 𝑓: 0.88 (3 hom.)
• Consequence: ENST00000392097.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.933 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
	ENST00000392097.5	n.669C>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.873 AC: 132723 AN: 152084 Hom.: 58143 Cov.: 32

Gnomad AFR AF: 0.941

Gnomad AMI AF: 0.836

Gnomad AMR AF: 0.867

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.875

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.878

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.844

Gnomad OTH AF: 0.855

GnomAD4 exome AF: 0.875 AC: 7 AN: 8 Hom.: 3 Cov.: 0 AF XY: 0.875 AC XY: 7 AN XY: 8

Gnomad4 AFR exome AF: 1.00

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 0.500

GnomAD4 genome AF: 0.873 AC: 132835 AN: 152202 Hom.: 58198 Cov.: 32 AF XY: 0.873 AC XY: 64908 AN XY: 74376

Gnomad4 AFR AF: 0.941

Gnomad4 AMR AF: 0.867

Gnomad4 ASJ AF: 0.761

Gnomad4 EAS AF: 0.875

Gnomad4 SAS AF: 0.799

Gnomad4 FIN AF: 0.878

Gnomad4 NFE AF: 0.844

Gnomad4 OTH AF: 0.855

Alfa AF: 0.843 Hom.: 77816

Bravo AF: 0.876

Asia WGS AF: 0.855 AC: 2975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.1
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2038024; hg19: chr1-169455982;