chr1-10824979-G-A

Position:

• chr1-10824979-G-A

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 0.102 in 152,246 control chromosomes in the GnomAD database, including 902 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 0.10 (902 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.270

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.15 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15532 AN: 152128 Hom.: 900 Cov.: 32

Gnomad AFR AF: 0.0565

Gnomad AMI AF: 0.0604

Gnomad AMR AF: 0.0766

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0857

Gnomad SAS AF: 0.160

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.131

Gnomad OTH AF: 0.105

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

GnomAD4 genome AF: 0.102 AC: 15534 AN: 152246 Hom.: 902 Cov.: 32 AF XY: 0.102 AC XY: 7624 AN XY: 74438

Gnomad4 AFR AF: 0.0563

Gnomad4 AMR AF: 0.0764

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.0855

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.104

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.110

Alfa AF: 0.118 Hom.: 187

Bravo AF: 0.0970

Asia WGS AF: 0.122 AC: 424 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.9
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2294750; hg19: chr1-10885036;