1-99317401-C-A

Variant names:

• chr1-99317401-C-A
• rs12743824

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 0.481 in 151,718 control chromosomes in the GnomAD database, including 17,762 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 (17762 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.636 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: 0.481 AC: 72886 AN: 151600 Hom.: 17738 Cov.: 32

Gnomad AFR AF: 0.498

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.572

Gnomad ASJ AF: 0.465

Gnomad EAS AF: 0.655

Gnomad SAS AF: 0.483

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.495

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

GnomAD4 genome AF: 0.481 AC: 72955 AN: 151718 Hom.: 17762 Cov.: 32 AF XY: 0.483 AC XY: 35795 AN XY: 74130

African (AFR) AF: 0.499 AC: 20628 AN: 41380

American (AMR) AF: 0.573 AC: 8713 AN: 15200

Ashkenazi Jewish (ASJ) AF: 0.465 AC: 1611 AN: 3464

East Asian (EAS) AF: 0.654 AC: 3375 AN: 5160

South Asian (SAS) AF: 0.483 AC: 2326 AN: 4816

European-Finnish (FIN) AF: 0.471 AC: 4949 AN: 10514

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.440 AC: 29849 AN: 67870

Other (OTH) AF: 0.494 AC: 1042 AN: 2110

Alfa AF: 0.457 Hom.: 31647

Bravo AF: 0.492

Asia WGS AF: 0.563 AC: 1955 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.9
DANN	Benign	0.47
PhyloP100		0.069

Splicing

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

Other links and lift over

dbSNP: rs12743824; hg19: chr1-99782957; COSMIC: COSV59977719;