rs1384383

chr7-41525395-C-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 0.078 in 150,896 control chromosomes in the GnomAD database, including 1,180 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 0.078 (1180 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360

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 (AFR) allele frequency at 95% confidence interval = 0.231 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0778 AC: 11737 AN: 150808 Hom.: 1177 Cov.: 31

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0405

Gnomad ASJ AF: 0.0127

Gnomad EAS AF: 0.000387

Gnomad SAS AF: 0.0126

Gnomad FIN AF: 0.0140

Gnomad MID AF: 0.0510

Gnomad NFE AF: 0.0165

Gnomad OTH AF: 0.0575

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

GnomAD4 genome AF: 0.0780 AC: 11765 AN: 150896 Hom.: 1180 Cov.: 31 AF XY: 0.0766 AC XY: 5642 AN XY: 73666

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.0404

Gnomad4 ASJ AF: 0.0127

Gnomad4 EAS AF: 0.000388

Gnomad4 SAS AF: 0.0124

Gnomad4 FIN AF: 0.0140

Gnomad4 NFE AF: 0.0165

Gnomad4 OTH AF: 0.0576

Alfa AF: 0.0530 Hom.: 103

Bravo AF: 0.0886

Asia WGS AF: 0.0210 AC: 76 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	3.8
Dann	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1384383; hg19: chr7-41564993;