chr1-208545397-C-T

Variant names:

• chr1-208545397-C-T
• rs10494900
• ENST00000846586.1:n.138+6402C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000846586.1(ENSG00000310018):​n.138+6402C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0184 in 152,178 control chromosomes in the GnomAD database, including 36 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 0.018 (36 hom., cov: 31)
• Consequence: ENSG00000310018 ENST00000846586.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.81
• Publications: 1 publications found

Genes affected

ENSG00000310018 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BS1: Variant frequency is greater than expected in population afr. GnomAd4 allele frequency = 0.0184 (2797/152178) while in subpopulation AFR AF = 0.0309 (1281/41516). AF 95% confidence interval is 0.0295. There are 36 homozygotes in GnomAd4. There are 1255 alleles in the male GnomAd4 subpopulation. Median coverage is 31. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 36 gene

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
ENSG00000310018	ENST00000846586.1	n.138+6402C>T		intron_variant	Intron 1 of 2
ENSG00000310018	ENST00000846587.1	n.118+6402C>T		intron_variant	Intron 1 of 1
ENSG00000310018	ENST00000846588.1	n.118+6402C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0184 AC: 2797 AN: 152060 Hom.: 36 Cov.: 31

Gnomad AFR AF: 0.0309

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0192

Gnomad ASJ AF: 0.0268

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.0214

Gnomad FIN AF: 0.000189

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0141

Gnomad OTH AF: 0.0225

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

GnomAD4 genome AF: 0.0184 AC: 2797 AN: 152178 Hom.: 36 Cov.: 31 AF XY: 0.0169 AC XY: 1255 AN XY: 74404

African (AFR) AF: 0.0309 AC: 1281 AN: 41516

American (AMR) AF: 0.0191 AC: 292 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0268 AC: 93 AN: 3470

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5164

South Asian (SAS) AF: 0.0214 AC: 103 AN: 4814

European-Finnish (FIN) AF: 0.000189 AC: 2 AN: 10610

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.0141 AC: 960 AN: 68006

Other (OTH) AF: 0.0223 AC: 47 AN: 2110

Alfa AF: 0.0141 Hom.: 29

Bravo AF: 0.0209

Asia WGS AF: 0.0120 AC: 42 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.012
DANN	Benign	0.78
PhyloP100		-2.8

Splicing

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

Other links and lift over

dbSNP: rs10494900; hg19: chr1-208718742;