rs6681231

chr1-186690727-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 0.218 in 152,088 control chromosomes in the GnomAD database, including 4,689 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 0.22 (4689 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.29

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 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: 0.218 AC: 33166 AN: 151972 Hom.: 4670 Cov.: 32

Gnomad AFR AF: 0.392

Gnomad AMI AF: 0.0804

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.234

Gnomad EAS AF: 0.0489

Gnomad SAS AF: 0.164

Gnomad FIN AF: 0.0871

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.158

Gnomad OTH AF: 0.221

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

GnomAD4 genome AF: 0.218 AC: 33223 AN: 152088 Hom.: 4689 Cov.: 32 AF XY: 0.213 AC XY: 15844 AN XY: 74362

Gnomad4 AFR AF: 0.392

Gnomad4 AMR AF: 0.186

Gnomad4 ASJ AF: 0.234

Gnomad4 EAS AF: 0.0486

Gnomad4 SAS AF: 0.164

Gnomad4 FIN AF: 0.0871

Gnomad4 NFE AF: 0.158

Gnomad4 OTH AF: 0.223

Alfa AF: 0.191 Hom.: 421

Bravo AF: 0.234

Asia WGS AF: 0.159 AC: 555 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.34
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6681231; hg19: chr1-186659859;