1-208798618-C-T

Variant names:

• chr1-208798618-C-T
• rs1182870
• ENST00000718977.1:n.315+23001G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000718977.1(ENSG00000293786):​n.315+23001G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.842 in 152,140 control chromosomes in the GnomAD database, including 54,778 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 0.84 (54778 hom., cov: 31)
• Consequence: ENSG00000293786 ENST00000718977.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.65
• Publications: 2 publications found

Genes affected

ENSG00000293786 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.937 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
ENSG00000293786	ENST00000718977.1	n.315+23001G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.842 AC: 128047 AN: 152022 Hom.: 54738 Cov.: 31

Gnomad AFR AF: 0.687

Gnomad AMI AF: 0.869

Gnomad AMR AF: 0.912

Gnomad ASJ AF: 0.961

Gnomad EAS AF: 0.944

Gnomad SAS AF: 0.960

Gnomad FIN AF: 0.890

Gnomad MID AF: 0.949

Gnomad NFE AF: 0.889

Gnomad OTH AF: 0.880

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

GnomAD4 genome AF: 0.842 AC: 128137 AN: 152140 Hom.: 54778 Cov.: 31 AF XY: 0.847 AC XY: 63003 AN XY: 74388

African (AFR) AF: 0.687 AC: 28496 AN: 41450

American (AMR) AF: 0.912 AC: 13933 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.961 AC: 3338 AN: 3472

East Asian (EAS) AF: 0.945 AC: 4894 AN: 5180

South Asian (SAS) AF: 0.960 AC: 4632 AN: 4824

European-Finnish (FIN) AF: 0.890 AC: 9436 AN: 10606

Middle Eastern (MID) AF: 0.946 AC: 278 AN: 294

European-Non Finnish (NFE) AF: 0.889 AC: 60480 AN: 68016

Other (OTH) AF: 0.882 AC: 1859 AN: 2108

Alfa AF: 0.889 Hom.: 92273

Bravo AF: 0.837

Asia WGS AF: 0.931 AC: 3238 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.092
DANN	Benign	0.34
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1182870; hg19: chr1-208971963;