1-224859471-T-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

ENSG00000286719 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000657178.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286719	ENST00000657178.1		n.77+21808A>G		intron	N/A

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

African (AFR) AF: 0.803 AC: 33332 AN: 41488

American (AMR) AF: 0.651 AC: 9927 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 1724 AN: 3470

East Asian (EAS) AF: 0.816 AC: 4215 AN: 5166

South Asian (SAS) AF: 0.644 AC: 3098 AN: 4812

European-Finnish (FIN) AF: 0.460 AC: 4851 AN: 10552

Middle Eastern (MID) AF: 0.432 AC: 127 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32168 AN: 67954

Other (OTH) AF: 0.560 AC: 1182 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.70
DANN	Benign	0.61
PhyloP100		-0.43

Splicing

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

Other links and lift over

dbSNP: rs2800237; hg19: chr1-225047173;