rs2448412

Variant names:

• chr5-157899441-T-C
• rs2448412

Your query was ambiguous. Multiple possible variants found:

• chr5-157899441-T-C
• chr5-157899441-T-G

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 0.117 in 152,220 control chromosomes in the GnomAD database, including 1,210 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 0.12 (1210 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.650

ACMG classification

Verdict is Benign. Variant got -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 = 0.18 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: 0.117 AC: 17868 AN: 152102 Hom.: 1211 Cov.: 33

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.0274

Gnomad AMR AF: 0.0864

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.0803

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.117 AC: 17884 AN: 152220 Hom.: 1210 Cov.: 33 AF XY: 0.119 AC XY: 8872 AN XY: 74422

Gnomad4 AFR AF: 0.183

Gnomad4 AMR AF: 0.0862

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.135

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.0803

Gnomad4 OTH AF: 0.118

Alfa AF: 0.0908 Hom.: 145

Bravo AF: 0.116

Asia WGS AF: 0.119 AC: 414 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	1.8
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2448412; hg19: chr5-157326449;