ENST00000657178.1:n.78-2952T>C

Variant names:

• chr1-224823940-A-G
• rs2662928
• ENST00000657178.1:n.78-2952T>C

Variant summary

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

The ENST00000657178.1(ENSG00000286719):​n.78-2952T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.915 in 152,260 control chromosomes in the GnomAD database, including 63,919 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 0.91 (63919 hom., cov: 32)
• Consequence: ENSG00000286719 ENST00000657178.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.863

Genes affected

ENSG00000286719 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.953 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.78-2952T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.915 AC: 139135 AN: 152142 Hom.: 63865 Cov.: 32

Gnomad AFR AF: 0.961

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.835

Gnomad ASJ AF: 0.927

Gnomad EAS AF: 0.762

Gnomad SAS AF: 0.810

Gnomad FIN AF: 0.910

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.923

Gnomad OTH AF: 0.912

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

GnomAD4 genome AF: 0.915 AC: 139248 AN: 152260 Hom.: 63919 Cov.: 32 AF XY: 0.909 AC XY: 67692 AN XY: 74434

Gnomad4 AFR AF: 0.961

Gnomad4 AMR AF: 0.835

Gnomad4 ASJ AF: 0.927

Gnomad4 EAS AF: 0.763

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.910

Gnomad4 NFE AF: 0.923

Gnomad4 OTH AF: 0.912

Alfa AF: 0.901 Hom.: 5718

Bravo AF: 0.911

Asia WGS AF: 0.794 AC: 2759 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.0060
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2662928; hg19: chr1-225011642;