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. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.904

Gnomad4 AMR AF: 0.803

Gnomad4 ASJ AF: 0.673

Gnomad4 EAS AF: 0.797

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.768

Gnomad4 NFE AF: 0.718

Gnomad4 OTH AF: 0.764

Alfa AF: 0.725 Hom.: 16360

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1458402; hg19: chr6-78262791;