rs7540934

Variant names:

• chr1-109941151-G-A
• rs7540934

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 0.379 in 151,924 control chromosomes in the GnomAD database, including 11,266 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 0.38 (11266 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0270

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.408 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: 0.379 AC: 57483 AN: 151806 Hom.: 11258 Cov.: 31

Gnomad AFR AF: 0.366

Gnomad AMI AF: 0.278

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.410

Gnomad EAS AF: 0.0584

Gnomad SAS AF: 0.273

Gnomad FIN AF: 0.459

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.395

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

GnomAD4 genome AF: 0.379 AC: 57506 AN: 151924 Hom.: 11266 Cov.: 31 AF XY: 0.376 AC XY: 27894 AN XY: 74226

Gnomad4 AFR AF: 0.366

Gnomad4 AMR AF: 0.347

Gnomad4 ASJ AF: 0.410

Gnomad4 EAS AF: 0.0587

Gnomad4 SAS AF: 0.275

Gnomad4 FIN AF: 0.459

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.391

Alfa AF: 0.399 Hom.: 26114

Bravo AF: 0.369

Asia WGS AF: 0.181 AC: 631 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	7.6
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: rs7540934; hg19: chr1-110483773;