rs1158408

Variant names:

• chr4-67250821-G-A
• rs1158408

Your query was ambiguous. Multiple possible variants found:

• chr4-67250821-G-A
• chr4-67250821-G-C

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 0.712 in 151,946 control chromosomes in the GnomAD database, including 39,066 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 0.71 (39066 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.507

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.778 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: 0.712 AC: 108102 AN: 151828 Hom.: 39067 Cov.: 31

Gnomad AFR AF: 0.572

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.731

Gnomad ASJ AF: 0.812

Gnomad EAS AF: 0.643

Gnomad SAS AF: 0.726

Gnomad FIN AF: 0.751

Gnomad MID AF: 0.845

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.736

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

GnomAD4 genome AF: 0.712 AC: 108137 AN: 151946 Hom.: 39066 Cov.: 31 AF XY: 0.709 AC XY: 52659 AN XY: 74278

Gnomad4 AFR AF: 0.572

Gnomad4 AMR AF: 0.731

Gnomad4 ASJ AF: 0.812

Gnomad4 EAS AF: 0.641

Gnomad4 SAS AF: 0.725

Gnomad4 FIN AF: 0.751

Gnomad4 NFE AF: 0.784

Gnomad4 OTH AF: 0.732

Alfa AF: 0.776 Hom.: 90565

Bravo AF: 0.705

Asia WGS AF: 0.670 AC: 2331 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.41
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1158408; hg19: chr4-68116539;