rs6686423

Variant names:

• chr1-157467720-G-A
• rs6686423

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 0.208 in 152,194 control chromosomes in the GnomAD database, including 4,144 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 0.21 (4144 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.224

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.29 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: 0.208 AC: 31670 AN: 152076 Hom.: 4147 Cov.: 33

Gnomad AFR AF: 0.0639

Gnomad AMI AF: 0.335

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.297

Gnomad EAS AF: 0.0931

Gnomad SAS AF: 0.0738

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.281

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.208 AC: 31673 AN: 152194 Hom.: 4144 Cov.: 33 AF XY: 0.207 AC XY: 15392 AN XY: 74402

Gnomad4 AFR AF: 0.0637

Gnomad4 AMR AF: 0.297

Gnomad4 ASJ AF: 0.297

Gnomad4 EAS AF: 0.0933

Gnomad4 SAS AF: 0.0741

Gnomad4 FIN AF: 0.249

Gnomad4 NFE AF: 0.281

Gnomad4 OTH AF: 0.226

Alfa AF: 0.267 Hom.: 5466

Bravo AF: 0.206

Asia WGS AF: 0.0790 AC: 278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.8
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: rs6686423; hg19: chr1-157437510;