chr1-10824979-G-A

Variant names:

• chr1-10824979-G-A
• rs2294750

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0563 AC: 2341 AN: 41556

American (AMR) AF: 0.0764 AC: 1170 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.128 AC: 444 AN: 3470

East Asian (EAS) AF: 0.0855 AC: 443 AN: 5180

South Asian (SAS) AF: 0.160 AC: 769 AN: 4820

European-Finnish (FIN) AF: 0.104 AC: 1105 AN: 10604

Middle Eastern (MID) AF: 0.160 AC: 47 AN: 294

European-Non Finnish (NFE) AF: 0.131 AC: 8928 AN: 67996

Other (OTH) AF: 0.110 AC: 232 AN: 2110

Alfa AF: 0.116 Hom.: 338

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
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs2294750; hg19: chr1-10885036;