rs1158408

chr4-67250821-G-Achr4-67250821-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;