1-170411339-A-G

Variant names:

• chr1-170411339-A-G
• rs6427247

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.267 in 151,844 control chromosomes in the GnomAD database, including 5,590 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 0.27 (5590 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.724
• Publications: 10 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.2).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.292 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: 0.267 AC: 40454 AN: 151726 Hom.: 5584 Cov.: 31

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.274

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.300

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.296

Gnomad OTH AF: 0.278

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

GnomAD4 genome AF: 0.267 AC: 40486 AN: 151844 Hom.: 5590 Cov.: 31 AF XY: 0.268 AC XY: 19889 AN XY: 74218

African (AFR) AF: 0.197 AC: 8157 AN: 41376

American (AMR) AF: 0.275 AC: 4196 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1048 AN: 3462

East Asian (EAS) AF: 0.298 AC: 1533 AN: 5150

South Asian (SAS) AF: 0.300 AC: 1448 AN: 4826

European-Finnish (FIN) AF: 0.295 AC: 3112 AN: 10540

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.296 AC: 20081 AN: 67900

Other (OTH) AF: 0.278 AC: 587 AN: 2110

Alfa AF: 0.289 Hom.: 28080

Bravo AF: 0.261

Asia WGS AF: 0.279 AC: 968 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.20
CADD	Benign	16
DANN	Benign	0.69
PhyloP100		0.72

Splicing

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

Other links and lift over

dbSNP: rs6427247; hg19: chr1-170380480;