rs1878658

chr6-137657249-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 0.149 in 152,238 control chromosomes in the GnomAD database, including 1,887 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 0.15 (1887 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.408

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.182 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: 0.150 AC: 22755 AN: 152120 Hom.: 1890 Cov.: 32

Gnomad AFR AF: 0.0768

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.0941

Gnomad SAS AF: 0.186

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.220

Gnomad NFE AF: 0.185

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.149 AC: 22740 AN: 152238 Hom.: 1887 Cov.: 32 AF XY: 0.147 AC XY: 10974 AN XY: 74428

Gnomad4 AFR AF: 0.0765

Gnomad4 AMR AF: 0.182

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.0939

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.185

Gnomad4 OTH AF: 0.154

Alfa AF: 0.171 Hom.: 553

Bravo AF: 0.151

Asia WGS AF: 0.114 AC: 397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
Cadd	Benign	5.4
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: rs1878658; hg19: chr6-137978386;