1-208680564-C-T

Variant names:

• chr1-208680564-C-T
• rs10494903
• ENST00000783296.1:n.240+313G>A

Variant summary

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

The ENST00000783296.1(ENSG00000302003):​n.240+313G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0155 in 152,282 control chromosomes in the GnomAD database, including 135 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 0.015 (135 hom., cov: 32)
• Consequence: ENSG00000302003 ENST00000783296.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.754
• Publications: 0 publications found

Genes affected

ENSG00000302003 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.178 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372892	XR_001738432.2	n.239-143G>A		intron_variant	Intron 3 of 4
LOC105372892	XR_001738434.2	n.6614-143G>A		intron_variant	Intron 2 of 3
LOC105372892	XR_001738435.2	n.6613+313G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302003	ENST00000783296.1	n.240+313G>A		intron_variant	Intron 3 of 3
ENSG00000302003	ENST00000783297.1	n.396+313G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0155 AC: 2363 AN: 152164 Hom.: 135 Cov.: 32

Gnomad AFR AF: 0.00169

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0286

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.189

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.00641

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.00200

Gnomad OTH AF: 0.0139

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

GnomAD4 genome AF: 0.0155 AC: 2359 AN: 152282 Hom.: 135 Cov.: 32 AF XY: 0.0185 AC XY: 1380 AN XY: 74466

African (AFR) AF: 0.00166 AC: 69 AN: 41574

American (AMR) AF: 0.0285 AC: 436 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0164 AC: 57 AN: 3472

East Asian (EAS) AF: 0.188 AC: 971 AN: 5168

South Asian (SAS) AF: 0.122 AC: 588 AN: 4818

European-Finnish (FIN) AF: 0.00641 AC: 68 AN: 10612

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.00200 AC: 136 AN: 68014

Other (OTH) AF: 0.0147 AC: 31 AN: 2112

Alfa AF: 0.00340 Hom.: 3

Bravo AF: 0.0161

Asia WGS AF: 0.154 AC: 532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.2
DANN	Benign	0.52
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs10494903; hg19: chr1-208853909;