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. The variant received -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
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.665 AC: 27572 AN: 41446

American (AMR) AF: 0.711 AC: 10869 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2645 AN: 3468

East Asian (EAS) AF: 0.715 AC: 3697 AN: 5172

South Asian (SAS) AF: 0.768 AC: 3710 AN: 4828

European-Finnish (FIN) AF: 0.778 AC: 8237 AN: 10590

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.780 AC: 53016 AN: 68006

Other (OTH) AF: 0.752 AC: 1586 AN: 2110

Alfa AF: 0.765 Hom.: 149331

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
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs6689305; hg19: chr1-100268991;