rs10494707

Positions:

• chr1-194596083-C-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 0.634 in 152,018 control chromosomes in the GnomAD database, including 32,076 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 0.63 (32076 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.884

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.194596083C>T		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.634 AC: 96365 AN: 151900 Hom.: 32080 Cov.: 32

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.829

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.748

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.566

Gnomad FIN AF: 0.662

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.670

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

GnomAD4 genome AF: 0.634 AC: 96380 AN: 152018 Hom.: 32076 Cov.: 32 AF XY: 0.628 AC XY: 46653 AN XY: 74310

Gnomad4 AFR AF: 0.440

Gnomad4 AMR AF: 0.580

Gnomad4 ASJ AF: 0.748

Gnomad4 EAS AF: 0.744

Gnomad4 SAS AF: 0.566

Gnomad4 FIN AF: 0.662

Gnomad4 NFE AF: 0.746

Gnomad4 OTH AF: 0.672

Alfa AF: 0.667 Hom.: 4333

Bravo AF: 0.620

Asia WGS AF: 0.628 AC: 2183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.077
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10494707; hg19: chr1-194565213;