rs1384383

Variant names:

• chr7-41525395-C-T
• rs1384383

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 0.078 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

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: 0.0778 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

African (AFR) AF: 0.235 AC: 9632 AN: 41006

American (AMR) AF: 0.0404 AC: 613 AN: 15184

Ashkenazi Jewish (ASJ) AF: 0.0127 AC: 44 AN: 3460

East Asian (EAS) AF: 0.000388 AC: 2 AN: 5150

South Asian (SAS) AF: 0.0124 AC: 59 AN: 4762

European-Finnish (FIN) AF: 0.0140 AC: 143 AN: 10190

Middle Eastern (MID) AF: 0.0445 AC: 13 AN: 292

European-Non Finnish (NFE) AF: 0.0165 AC: 1121 AN: 67856

Other (OTH) AF: 0.0576 AC: 120 AN: 2084

Alfa AF: 0.0474 Hom.: 184

Bravo AF: 0.0886

Asia WGS AF: 0.0210 AC: 76 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.8
DANN	Benign	0.51
PhyloP100		0.036

Splicing

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

Other links and lift over

dbSNP: rs1384383; hg19: chr7-41564993;