rs1021639

Variant names:

• chr1-214230538-G-A
• rs1021639
• ENST00000722830.1:n.292-12757C>T

Variant summary

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

The ENST00000722830.1(ENSG00000294336):​n.292-12757C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.778 in 151,972 control chromosomes in the GnomAD database, including 46,134 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 0.78 (46134 hom., cov: 31)
• Consequence: ENSG00000294336 ENST00000722830.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286
• Publications: 2 publications found

Genes affected

ENSG00000294336 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.799 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
ENSG00000294336	ENST00000722830.1	n.292-12757C>T		intron_variant	Intron 2 of 2
ENSG00000294336	ENST00000722831.1	n.264-12757C>T		intron_variant	Intron 2 of 2
ENSG00000294353	ENST00000723060.1	n.426+712G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.779 AC: 118229 AN: 151856 Hom.: 46105 Cov.: 31

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.859

Gnomad AMR AF: 0.799

Gnomad ASJ AF: 0.826

Gnomad EAS AF: 0.706

Gnomad SAS AF: 0.688

Gnomad FIN AF: 0.808

Gnomad MID AF: 0.826

Gnomad NFE AF: 0.805

Gnomad OTH AF: 0.800

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.778 AC: 118306 AN: 151972 Hom.: 46134 Cov.: 31 AF XY: 0.778 AC XY: 57817 AN XY: 74290

African (AFR) AF: 0.732 AC: 30287 AN: 41364

American (AMR) AF: 0.799 AC: 12215 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.826 AC: 2869 AN: 3472

East Asian (EAS) AF: 0.706 AC: 3633 AN: 5148

South Asian (SAS) AF: 0.689 AC: 3318 AN: 4814

European-Finnish (FIN) AF: 0.808 AC: 8554 AN: 10592

Middle Eastern (MID) AF: 0.833 AC: 245 AN: 294

European-Non Finnish (NFE) AF: 0.805 AC: 54724 AN: 67992

Other (OTH) AF: 0.797 AC: 1681 AN: 2108

Alfa AF: 0.795 Hom.: 16346

Bravo AF: 0.779

Asia WGS AF: 0.673 AC: 2341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.57
DANN	Benign	0.56
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1021639; hg19: chr1-214403881;