rs1405443

Variant names:

• chr7-54097534-A-G
• rs1405443

Your query was ambiguous. Multiple possible variants found:

• chr7-54097534-A-G
• chr7-54097534-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 0.767 in 152,058 control chromosomes in the GnomAD database, including 46,266 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 0.77 (46266 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.495
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.866 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.767 AC: 116532 AN: 151940 Hom.: 46246 Cov.: 32

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.957

Gnomad AMR AF: 0.821

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.757

Gnomad SAS AF: 0.739

Gnomad FIN AF: 0.846

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.872

Gnomad OTH AF: 0.793

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

GnomAD4 genome AF: 0.767 AC: 116585 AN: 152058 Hom.: 46266 Cov.: 32 AF XY: 0.766 AC XY: 56949 AN XY: 74334

African (AFR) AF: 0.541 AC: 22413 AN: 41452

American (AMR) AF: 0.822 AC: 12544 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.896 AC: 3111 AN: 3472

East Asian (EAS) AF: 0.757 AC: 3906 AN: 5158

South Asian (SAS) AF: 0.740 AC: 3565 AN: 4816

European-Finnish (FIN) AF: 0.846 AC: 8967 AN: 10596

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.872 AC: 59293 AN: 67984

Other (OTH) AF: 0.794 AC: 1674 AN: 2108

Alfa AF: 0.840 Hom.: 164664

Bravo AF: 0.759

Asia WGS AF: 0.731 AC: 2538 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.3
DANN	Benign	0.58
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs1405443; hg19: chr7-54165227;