chr1-169486744-C-A

Variant names:

• chr1-169486744-C-A
• rs2038024
• ENST00000392097.6:n.673C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000392097.6(ENSG00000213062):​n.673C>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 ENST00000392097.6 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.112
• Publications: 11 publications found

Genes affected

ENSG00000213062 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000392097.6. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000213062	ENST00000392097.6	TSL:6	n.673C>A		non_coding_transcript_exon	Exon 1 of 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

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 1.00 AC: 4 AN: 4

Other (OTH) AF: 0.500 AC: 1 AN: 2

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

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

African (AFR) AF: 0.941 AC: 39106 AN: 41548

American (AMR) AF: 0.867 AC: 13261 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2643 AN: 3472

East Asian (EAS) AF: 0.875 AC: 4525 AN: 5170

South Asian (SAS) AF: 0.799 AC: 3852 AN: 4824

European-Finnish (FIN) AF: 0.878 AC: 9289 AN: 10574

Middle Eastern (MID) AF: 0.731 AC: 215 AN: 294

European-Non Finnish (NFE) AF: 0.844 AC: 57373 AN: 67998

Other (OTH) AF: 0.855 AC: 1809 AN: 2116

Alfa AF: 0.847 Hom.: 98094

Bravo AF: 0.876

Asia WGS AF: 0.855 AC: 2975 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.1
DANN	Benign	0.64
PhyloP100		-0.11

Splicing

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

Other links and lift over

dbSNP: rs2038024; hg19: chr1-169455982;