rs6689305

Variant names:

• chr1-99803435-G-A
• rs6689305

Your query was ambiguous. Multiple possible variants found:

• chr1-99803435-G-A
• chr1-99803435-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 0.738 in 152,108 control chromosomes in the GnomAD database, including 41,677 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 0.74 (41677 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.774 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: 0.738 AC: 112241 AN: 151990 Hom.: 41649 Cov.: 32

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.849

Gnomad AMR AF: 0.711

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.715

Gnomad SAS AF: 0.767

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.780

Gnomad OTH AF: 0.747

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

GnomAD4 genome AF: 0.738 AC: 112325 AN: 152108 Hom.: 41677 Cov.: 32 AF XY: 0.739 AC XY: 54944 AN XY: 74368

Gnomad4 AFR AF: 0.665

Gnomad4 AMR AF: 0.711

Gnomad4 ASJ AF: 0.763

Gnomad4 EAS AF: 0.715

Gnomad4 SAS AF: 0.768

Gnomad4 FIN AF: 0.778

Gnomad4 NFE AF: 0.780

Gnomad4 OTH AF: 0.752

Alfa AF: 0.773 Hom.: 91694

Bravo AF: 0.731

Asia WGS AF: 0.733 AC: 2550 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	4.5
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6689305; hg19: chr1-100268991;