rs1458246

Variant names:

• chr4-68952364-C-A
• rs1458246

Your query was ambiguous. Multiple possible variants found:

• chr4-68952364-C-A
• chr4-68952364-C-T

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 0.73 in 151,762 control chromosomes in the GnomAD database, including 42,044 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 0.73 (42044 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.57
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.852 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: 0.730 AC: 110724 AN: 151644 Hom.: 42036 Cov.: 33

Gnomad AFR AF: 0.529

Gnomad AMI AF: 0.828

Gnomad AMR AF: 0.659

Gnomad ASJ AF: 0.855

Gnomad EAS AF: 0.677

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.740

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.858

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.730 AC: 110759 AN: 151762 Hom.: 42044 Cov.: 33 AF XY: 0.725 AC XY: 53743 AN XY: 74160

African (AFR) AF: 0.528 AC: 21866 AN: 41378

American (AMR) AF: 0.659 AC: 10033 AN: 15236

Ashkenazi Jewish (ASJ) AF: 0.855 AC: 2968 AN: 3470

East Asian (EAS) AF: 0.677 AC: 3456 AN: 5104

South Asian (SAS) AF: 0.802 AC: 3872 AN: 4826

European-Finnish (FIN) AF: 0.740 AC: 7802 AN: 10548

Middle Eastern (MID) AF: 0.741 AC: 218 AN: 294

European-Non Finnish (NFE) AF: 0.858 AC: 58243 AN: 67884

Other (OTH) AF: 0.733 AC: 1546 AN: 2110

Alfa AF: 0.722 Hom.: 5061

Bravo AF: 0.709

Asia WGS AF: 0.713 AC: 2478 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.12
DANN	Benign	0.47
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs1458246; hg19: chr4-69818082;