chr1-208289776-G-A

Variant names:

• chr1-208289776-G-A
• rs10494894
• ENST00000798836.1:n.366+29001G>A

Variant summary

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

The ENST00000798836.1(ENSG00000304011):​n.366+29001G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0549 in 152,262 control chromosomes in the GnomAD database, including 591 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 0.055 (591 hom., cov: 32)
• Consequence: ENSG00000304011 ENST00000798836.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380
• Publications: 1 publications found

Genes affected

ENSG00000304011 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372889	XR_922508.2	n.357+29001G>A		intron_variant	Intron 4 of 5
LOC105372889	XR_922509.2	n.354+29001G>A		intron_variant	Intron 4 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000304011	ENST00000798836.1	n.366+29001G>A		intron_variant	Intron 3 of 6
ENSG00000304011	ENST00000798837.1	n.403+29001G>A		intron_variant	Intron 4 of 6
ENSG00000304011	ENST00000798838.1	n.507+29001G>A		intron_variant	Intron 4 of 5

Frequencies

GnomAD3 genomes AF: 0.0549 AC: 8350 AN: 152144 Hom.: 588 Cov.: 32

Gnomad AFR AF: 0.149

Gnomad AMI AF: 0.00219

Gnomad AMR AF: 0.0243

Gnomad ASJ AF: 0.0346

Gnomad EAS AF: 0.130

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.00328

Gnomad OTH AF: 0.0382

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

GnomAD4 genome AF: 0.0549 AC: 8359 AN: 152262 Hom.: 591 Cov.: 32 AF XY: 0.0555 AC XY: 4130 AN XY: 74454

African (AFR) AF: 0.149 AC: 6186 AN: 41546

American (AMR) AF: 0.0242 AC: 370 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0346 AC: 120 AN: 3472

East Asian (EAS) AF: 0.129 AC: 668 AN: 5168

South Asian (SAS) AF: 0.144 AC: 693 AN: 4818

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10624

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00328 AC: 223 AN: 68012

Other (OTH) AF: 0.0416 AC: 88 AN: 2116

Alfa AF: 0.00247 Hom.: 1

Bravo AF: 0.0585

Asia WGS AF: 0.113 AC: 395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.0
DANN	Benign	0.67
PhyloP100		-0.038

Splicing

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

Other links and lift over

dbSNP: rs10494894; hg19: chr1-208463121;