rs1358716

Positions:

• chr6-139124867-A-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 0.561 in 151,902 control chromosomes in the GnomAD database, including 24,908 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 0.56 (24908 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.05

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.605 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.561 AC: 85139 AN: 151784 Hom.: 24900 Cov.: 31

Gnomad AFR AF: 0.611

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.628

Gnomad EAS AF: 0.0405

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.588

Gnomad OTH AF: 0.588

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

GnomAD4 genome AF: 0.561 AC: 85185 AN: 151902 Hom.: 24908 Cov.: 31 AF XY: 0.551 AC XY: 40864 AN XY: 74208

Gnomad4 AFR AF: 0.611

Gnomad4 AMR AF: 0.515

Gnomad4 ASJ AF: 0.628

Gnomad4 EAS AF: 0.0406

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.588

Gnomad4 OTH AF: 0.581

Alfa AF: 0.586 Hom.: 24146

Bravo AF: 0.562

Asia WGS AF: 0.246 AC: 859 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.16
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1358716; hg19: chr6-139446004; COSMIC: COSV60286487;