rs10782529

Variant names:

• chr1-84802560-C-T
• rs10782529

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 0.672 in 151,928 control chromosomes in the GnomAD database, including 34,701 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 0.67 (34701 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.41
• Publications: 9 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.762 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: 0.672 AC: 102081 AN: 151810 Hom.: 34685 Cov.: 32

Gnomad AFR AF: 0.769

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.560

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.693

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.672 AC: 102136 AN: 151928 Hom.: 34701 Cov.: 32 AF XY: 0.670 AC XY: 49789 AN XY: 74258

African (AFR) AF: 0.769 AC: 31849 AN: 41408

American (AMR) AF: 0.559 AC: 8537 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 2560 AN: 3468

East Asian (EAS) AF: 0.663 AC: 3410 AN: 5144

South Asian (SAS) AF: 0.694 AC: 3346 AN: 4820

European-Finnish (FIN) AF: 0.627 AC: 6614 AN: 10550

Middle Eastern (MID) AF: 0.653 AC: 192 AN: 294

European-Non Finnish (NFE) AF: 0.644 AC: 43745 AN: 67956

Other (OTH) AF: 0.667 AC: 1404 AN: 2106

Alfa AF: 0.656 Hom.: 60286

Bravo AF: 0.670

Asia WGS AF: 0.664 AC: 2310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.45
DANN	Benign	0.18
PhyloP100		-2.4

Splicing

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

Other links and lift over

dbSNP: rs10782529; hg19: chr1-85268243;