7-54097534-A-G

Variant names:

• chr7-54097534-A-G
• rs1405443

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 0.767 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.767 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

Gnomad4 AFR AF: 0.541

Gnomad4 AMR AF: 0.822

Gnomad4 ASJ AF: 0.896

Gnomad4 EAS AF: 0.757

Gnomad4 SAS AF: 0.740

Gnomad4 FIN AF: 0.846

Gnomad4 NFE AF: 0.872

Gnomad4 OTH AF: 0.794

Alfa AF: 0.857 Hom.: 111449

Bravo AF: 0.759

Asia WGS AF: 0.731 AC: 2538 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1405443; hg19: chr7-54165227;