rs1458402

Variant names:

• chr6-77553074-A-G
• rs1458402

Your query was ambiguous. Multiple possible variants found:

• chr6-77553074-A-G
• chr6-77553074-A-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 0.783 in 152,122 control chromosomes in the GnomAD database, including 47,264 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 0.78 (47264 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.593
• Publications: 7 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 = 0.896 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: 0.783 AC: 119007 AN: 152002 Hom.: 47183 Cov.: 33

Gnomad AFR AF: 0.904

Gnomad AMI AF: 0.740

Gnomad AMR AF: 0.803

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.796

Gnomad SAS AF: 0.729

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.618

Gnomad NFE AF: 0.718

Gnomad OTH AF: 0.761

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

GnomAD4 genome AF: 0.783 AC: 119145 AN: 152122 Hom.: 47264 Cov.: 33 AF XY: 0.784 AC XY: 58319 AN XY: 74358

African (AFR) AF: 0.904 AC: 37536 AN: 41536

American (AMR) AF: 0.803 AC: 12261 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2338 AN: 3472

East Asian (EAS) AF: 0.797 AC: 4108 AN: 5154

South Asian (SAS) AF: 0.729 AC: 3517 AN: 4826

European-Finnish (FIN) AF: 0.768 AC: 8121 AN: 10576

Middle Eastern (MID) AF: 0.613 AC: 179 AN: 292

European-Non Finnish (NFE) AF: 0.718 AC: 48797 AN: 67984

Other (OTH) AF: 0.764 AC: 1613 AN: 2110

Alfa AF: 0.727 Hom.: 18673

Bravo AF: 0.790

Asia WGS AF: 0.800 AC: 2781 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	1.1
DANN	Benign	0.33
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs1458402; hg19: chr6-78262791;