rs6703170

Variant names:

• chr1-226787569-A-G
• rs6703170

Your query was ambiguous. Multiple possible variants found:

• chr1-226787569-A-G
• chr1-226787569-A-T

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 0.222 in 152,090 control chromosomes in the GnomAD database, including 4,296 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 0.22 (4296 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.21
• Publications: 7 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.291 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.222 AC: 33697 AN: 151972 Hom.: 4296 Cov.: 31

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.154

Gnomad EAS AF: 0.0994

Gnomad SAS AF: 0.288

Gnomad FIN AF: 0.301

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.295

Gnomad OTH AF: 0.182

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

GnomAD4 genome AF: 0.222 AC: 33703 AN: 152090 Hom.: 4296 Cov.: 31 AF XY: 0.222 AC XY: 16539 AN XY: 74352

African (AFR) AF: 0.118 AC: 4895 AN: 41490

American (AMR) AF: 0.166 AC: 2530 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.154 AC: 534 AN: 3472

East Asian (EAS) AF: 0.0995 AC: 515 AN: 5178

South Asian (SAS) AF: 0.286 AC: 1377 AN: 4812

European-Finnish (FIN) AF: 0.301 AC: 3177 AN: 10560

Middle Eastern (MID) AF: 0.139 AC: 41 AN: 294

European-Non Finnish (NFE) AF: 0.295 AC: 20034 AN: 67982

Other (OTH) AF: 0.187 AC: 395 AN: 2112

Alfa AF: 0.260 Hom.: 10360

Bravo AF: 0.206

Asia WGS AF: 0.236 AC: 819 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.077
DANN	Benign	0.30
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs6703170; hg19: chr1-226975270;