rs6659759

Positions:

• 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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;