rs1447386

Variant names:

• chr5-99130268-G-C
• rs1447386

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 0.0314 in 152,210 control chromosomes in the GnomAD database, including 211 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 0.031 (211 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00100
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0987 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: 0.0313 AC: 4766 AN: 152092 Hom.: 210 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.00879

Gnomad AMR AF: 0.00911

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.00366

Gnomad SAS AF: 0.0172

Gnomad FIN AF: 0.0000943

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.00363

Gnomad OTH AF: 0.0139

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

GnomAD4 genome AF: 0.0314 AC: 4777 AN: 152210 Hom.: 211 Cov.: 32 AF XY: 0.0304 AC XY: 2265 AN XY: 74418

African (AFR) AF: 0.101 AC: 4205 AN: 41518

American (AMR) AF: 0.00910 AC: 139 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0101 AC: 35 AN: 3470

East Asian (EAS) AF: 0.00367 AC: 19 AN: 5178

South Asian (SAS) AF: 0.0170 AC: 82 AN: 4818

European-Finnish (FIN) AF: 0.0000943 AC: 1 AN: 10608

Middle Eastern (MID) AF: 0.0408 AC: 12 AN: 294

European-Non Finnish (NFE) AF: 0.00363 AC: 247 AN: 68026

Other (OTH) AF: 0.0137 AC: 29 AN: 2114

Alfa AF: 0.0200 Hom.: 13

Bravo AF: 0.0353

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.9
DANN	Benign	0.12
PhyloP100		-0.0010

Splicing

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

Other links and lift over

dbSNP: rs1447386; hg19: chr5-98465972;