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. The variant received -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
• Publications: 0 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0304 AC: 1265 AN: 41570

American (AMR) AF: 0.104 AC: 1587 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.167 AC: 580 AN: 3468

East Asian (EAS) AF: 0.296 AC: 1532 AN: 5180

South Asian (SAS) AF: 0.233 AC: 1124 AN: 4824

European-Finnish (FIN) AF: 0.0968 AC: 1026 AN: 10604

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.135 AC: 9201 AN: 68010

Other (OTH) AF: 0.127 AC: 268 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.2
DANN	Benign	0.82
PhyloP100		-0.0030

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6680654;

hg19: chr1-119424027;