rs6681231

Variant names:

• chr1-186690727-G-C
• rs6681231

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;