rs859665

Variant names:

• chr1-172695302-A-G
• rs859665

Your query was ambiguous. Multiple possible variants found:

• chr1-172695302-A-G
• chr1-172695302-A-T

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 0.388 in 151,870 control chromosomes in the GnomAD database, including 12,911 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 0.39 (12911 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.591

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.577 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: 0.388 AC: 58837 AN: 151752 Hom.: 12901 Cov.: 31

Gnomad AFR AF: 0.583

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.355

Gnomad EAS AF: 0.00889

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.303

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.341

Gnomad OTH AF: 0.364

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

GnomAD4 genome AF: 0.388 AC: 58871 AN: 151870 Hom.: 12911 Cov.: 31 AF XY: 0.380 AC XY: 28209 AN XY: 74256

Gnomad4 AFR AF: 0.583

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.355

Gnomad4 EAS AF: 0.00891

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.303

Gnomad4 NFE AF: 0.341

Gnomad4 OTH AF: 0.358

Alfa AF: 0.322 Hom.: 4699

Bravo AF: 0.399

Asia WGS AF: 0.151 AC: 529 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.38
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs859665; hg19: chr1-172664442; COSMIC: COSV56922091;