rs10494894

Positions:

• chr1-208289776-G-A
• chr1-208289776-G-T

Variant summary

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

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0380

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.208289776G>A		intergenic_region
LOC105372889	XR_922508.2	n.357+29001G>A		intron_variant
LOC105372889	XR_922509.2	n.354+29001G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.149

Gnomad4 AMR AF: 0.0242

Gnomad4 ASJ AF: 0.0346

Gnomad4 EAS AF: 0.129

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00328

Gnomad4 OTH AF: 0.0416

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494894; hg19: chr1-208463121;