chr1-24966710-A-G

Variant names:

• chr1-24966710-A-G
• rs11249212

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 0.477 in 152,196 control chromosomes in the GnomAD database, including 18,689 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 0.48 (18689 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.443
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 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: 0.477 AC: 72527 AN: 152078 Hom.: 18662 Cov.: 34

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.690

Gnomad AMR AF: 0.640

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.511

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

GnomAD4 genome AF: 0.477 AC: 72572 AN: 152196 Hom.: 18689 Cov.: 34 AF XY: 0.492 AC XY: 36615 AN XY: 74404

African (AFR) AF: 0.287 AC: 11916 AN: 41516

American (AMR) AF: 0.641 AC: 9801 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1768 AN: 3472

East Asian (EAS) AF: 0.707 AC: 3668 AN: 5186

South Asian (SAS) AF: 0.677 AC: 3270 AN: 4830

European-Finnish (FIN) AF: 0.577 AC: 6108 AN: 10592

Middle Eastern (MID) AF: 0.545 AC: 159 AN: 292

European-Non Finnish (NFE) AF: 0.503 AC: 34164 AN: 67984

Other (OTH) AF: 0.516 AC: 1089 AN: 2110

Alfa AF: 0.479 Hom.: 2357

Bravo AF: 0.474

Asia WGS AF: 0.693 AC: 2408 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	0.69
DANN	Benign	0.60
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs11249212; hg19: chr1-25293201;