rs6426893

Variant names:

• chr1-165058105-G-A
• rs6426893

Your query was ambiguous. Multiple possible variants found:

• chr1-165058105-G-A
• chr1-165058105-G-C
• chr1-165058105-G-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 0.656 in 152,206 control chromosomes in the GnomAD database, including 37,826 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 0.66 (37826 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.602
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.817 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: 0.657 AC: 99871 AN: 152088 Hom.: 37811 Cov.: 33

Gnomad AFR AF: 0.247

Gnomad AMI AF: 0.929

Gnomad AMR AF: 0.773

Gnomad ASJ AF: 0.632

Gnomad EAS AF: 0.837

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.873

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.823

Gnomad OTH AF: 0.685

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

GnomAD4 genome AF: 0.656 AC: 99900 AN: 152206 Hom.: 37826 Cov.: 33 AF XY: 0.661 AC XY: 49169 AN XY: 74412

African (AFR) AF: 0.246 AC: 10222 AN: 41496

American (AMR) AF: 0.774 AC: 11832 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.632 AC: 2192 AN: 3468

East Asian (EAS) AF: 0.837 AC: 4338 AN: 5180

South Asian (SAS) AF: 0.745 AC: 3592 AN: 4822

European-Finnish (FIN) AF: 0.873 AC: 9263 AN: 10610

Middle Eastern (MID) AF: 0.585 AC: 172 AN: 294

European-Non Finnish (NFE) AF: 0.823 AC: 55985 AN: 68018

Other (OTH) AF: 0.689 AC: 1457 AN: 2116

Alfa AF: 0.764 Hom.: 75191

Bravo AF: 0.634

Asia WGS AF: 0.767 AC: 2666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.16
DANN	Benign	0.38
PhyloP100		-0.60

Splicing

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

Other links and lift over

dbSNP: rs6426893; hg19: chr1-165027342;