rs6680654

Variant names:

• chr1-118881404-T-A
• rs6680654

Your query was ambiguous. Multiple possible variants found:

• chr1-118881404-T-A
• chr1-118881404-T-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 0.11 in 152,264 control chromosomes in the GnomAD database, including 1,172 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 0.11 (1172 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.283 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: 0.110 AC: 16679 AN: 152146 Hom.: 1171 Cov.: 33

Gnomad AFR AF: 0.0305

Gnomad AMI AF: 0.0636

Gnomad AMR AF: 0.104

Gnomad ASJ AF: 0.167

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.0968

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.125

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

GnomAD4 genome AF: 0.110 AC: 16677 AN: 152264 Hom.: 1172 Cov.: 33 AF XY: 0.111 AC XY: 8236 AN XY: 74436

Gnomad4 AFR AF: 0.0304

Gnomad4 AMR AF: 0.104

Gnomad4 ASJ AF: 0.167

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.0968

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.127

Alfa AF: 0.120 Hom.: 132

Bravo AF: 0.104

Asia WGS AF: 0.236 AC: 820 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.2
DANN	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6680654; hg19: chr1-119424027;