ENST00000657178.1:n.77+7552T>C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 7 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.896 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286719	ENST00000657178.1		n.77+7552T>C		intron	N/A

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

African (AFR) AF: 0.751 AC: 31163 AN: 41494

American (AMR) AF: 0.693 AC: 10593 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.543 AC: 1884 AN: 3468

East Asian (EAS) AF: 0.918 AC: 4757 AN: 5184

South Asian (SAS) AF: 0.756 AC: 3646 AN: 4824

European-Finnish (FIN) AF: 0.540 AC: 5704 AN: 10568

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.553 AC: 37615 AN: 67988

Other (OTH) AF: 0.615 AC: 1299 AN: 2112

Alfa AF: 0.577 Hom.: 43469

Bravo AF: 0.655

Asia WGS AF: 0.843 AC: 2930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.8
DANN	Benign	0.64
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs2800230; hg19: chr1-225061429;