rs2800230

Variant names:

• chr1-224873727-A-G
• rs2800230
• ENST00000657178.1:n.77+7552T>C

Your query was ambiguous. Multiple possible variants found:

• chr1-224873727-A-G
• chr1-224873727-A-T

Variant summary

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

The ENST00000657178.1(ENSG00000286719):​n.77+7552T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.64 in 152,116 control chromosomes in the GnomAD database, including 32,031 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 0.64 (32031 hom., cov: 33)
• Consequence: ENSG00000286719 ENST00000657178.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

Genes affected

ENSG00000286719 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.896 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+7552T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.639 AC: 97185 AN: 151998 Hom.: 31988 Cov.: 33

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.693

Gnomad ASJ AF: 0.543

Gnomad EAS AF: 0.918

Gnomad SAS AF: 0.757

Gnomad FIN AF: 0.540

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.640 AC: 97282 AN: 152116 Hom.: 32031 Cov.: 33 AF XY: 0.643 AC XY: 47810 AN XY: 74362

Gnomad4 AFR AF: 0.751

Gnomad4 AMR AF: 0.693

Gnomad4 ASJ AF: 0.543

Gnomad4 EAS AF: 0.918

Gnomad4 SAS AF: 0.756

Gnomad4 FIN AF: 0.540

Gnomad4 NFE AF: 0.553

Gnomad4 OTH AF: 0.615

Alfa AF: 0.570 Hom.: 33420

Bravo AF: 0.655

Asia WGS AF: 0.843 AC: 2930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.8
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: rs2800230; hg19: chr1-225061429;