rs6659759

Variant names:

• chr1-162067819-T-C
• rs6659759

Your query was ambiguous. Multiple possible variants found:

• chr1-162067819-T-C
• chr1-162067819-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 0.346 in 152,072 control chromosomes in the GnomAD database, including 9,532 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 0.35 (9532 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.246

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.617 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: 0.346 AC: 52557 AN: 151954 Hom.: 9532 Cov.: 32

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.352

Gnomad AMR AF: 0.331

Gnomad ASJ AF: 0.344

Gnomad EAS AF: 0.535

Gnomad SAS AF: 0.638

Gnomad FIN AF: 0.350

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.337

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

GnomAD4 genome AF: 0.346 AC: 52580 AN: 152072 Hom.: 9532 Cov.: 32 AF XY: 0.353 AC XY: 26236 AN XY: 74326

Gnomad4 AFR AF: 0.376

Gnomad4 AMR AF: 0.331

Gnomad4 ASJ AF: 0.344

Gnomad4 EAS AF: 0.534

Gnomad4 SAS AF: 0.636

Gnomad4 FIN AF: 0.350

Gnomad4 NFE AF: 0.296

Gnomad4 OTH AF: 0.341

Alfa AF: 0.317 Hom.: 997

Bravo AF: 0.337

Asia WGS AF: 0.578 AC: 2008 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.3
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6659759; hg19: chr1-162037609;