rs2407103

Variant names:

• chr8-37094396-A-G
• rs2407103

Your query was ambiguous. Multiple possible variants found:

• chr8-37094396-A-G
• chr8-37094396-A-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 0.1 in 152,290 control chromosomes in the GnomAD database, including 886 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 0.10 (886 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.504

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.239 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: 0.100 AC: 15214 AN: 152172 Hom.: 882 Cov.: 33

Gnomad AFR AF: 0.0914

Gnomad AMI AF: 0.0297

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.100

Gnomad EAS AF: 0.251

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0832

Gnomad OTH AF: 0.0937

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

GnomAD4 genome AF: 0.100 AC: 15228 AN: 152290 Hom.: 886 Cov.: 33 AF XY: 0.103 AC XY: 7663 AN XY: 74470

Gnomad4 AFR AF: 0.0913

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.100

Gnomad4 EAS AF: 0.251

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.0832

Gnomad4 OTH AF: 0.0951

Alfa AF: 0.0867 Hom.: 696

Bravo AF: 0.104

Asia WGS AF: 0.189 AC: 659 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.2
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2407103; hg19: chr8-36951914;