rs6683557

Positions:

• chr1-154879831-C-G
• chr1-154879831-C-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 0.526 in 151,882 control chromosomes in the GnomAD database, including 22,322 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 0.53 (22322 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00800

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.154879831C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79855 AN: 151764 Hom.: 22286 Cov.: 30

Gnomad AFR AF: 0.646

Gnomad AMI AF: 0.309

Gnomad AMR AF: 0.589

Gnomad ASJ AF: 0.513

Gnomad EAS AF: 0.880

Gnomad SAS AF: 0.627

Gnomad FIN AF: 0.419

Gnomad MID AF: 0.599

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.526 AC: 79940 AN: 151882 Hom.: 22322 Cov.: 30 AF XY: 0.532 AC XY: 39456 AN XY: 74212

Gnomad4 AFR AF: 0.646

Gnomad4 AMR AF: 0.589

Gnomad4 ASJ AF: 0.513

Gnomad4 EAS AF: 0.879

Gnomad4 SAS AF: 0.626

Gnomad4 FIN AF: 0.419

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.512

Alfa AF: 0.466 Hom.: 2171

Bravo AF: 0.544

Asia WGS AF: 0.747 AC: 2594 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	1.6
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: rs6683557; hg19: chr1-154852307;