rs2038024

Variant names:

• chr1-169486744-C-A
• rs2038024
• ENST00000392097.5:n.669C>A

Your query was ambiguous. Multiple possible variants found:

• chr1-169486744-C-A
• chr1-169486744-C-G
• chr1-169486744-C-T

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: ENSG00000213062 ENST00000392097.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112

Genes affected

ENSG00000213062 (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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000213062	ENST00000392097.5	n.669C>A		non_coding_transcript_exon_variant	Exon 1 of 1	6

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;