1-224859471-T-C

Variant names:

• chr1-224859471-T-C
• rs2800237
• ENST00000657178.1:n.77+21808A>G

Variant summary

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

The ENST00000657178.1(ENSG00000286719):​n.77+21808A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 152,014 control chromosomes in the GnomAD database, including 29,139 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 0.60 (29139 hom., cov: 31)
• Consequence: ENSG00000286719 ENST00000657178.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.431

Genes affected

ENSG00000286719 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.796 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
ENSG00000286719	ENST00000657178.1	n.77+21808A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.599 AC: 91010 AN: 151896 Hom.: 29109 Cov.: 31

Gnomad AFR AF: 0.804

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.497

Gnomad EAS AF: 0.817

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.563

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

GnomAD4 genome AF: 0.599 AC: 91086 AN: 152014 Hom.: 29139 Cov.: 31 AF XY: 0.601 AC XY: 44658 AN XY: 74286

Gnomad4 AFR AF: 0.803

Gnomad4 AMR AF: 0.651

Gnomad4 ASJ AF: 0.497

Gnomad4 EAS AF: 0.816

Gnomad4 SAS AF: 0.644

Gnomad4 FIN AF: 0.460

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.560

Alfa AF: 0.349 Hom.: 802

Bravo AF: 0.624

Asia WGS AF: 0.728 AC: 2533 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.70
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: rs2800237; hg19: chr1-225047173;