rs6688672

Positions:

• chr1-102003524-C-A
• chr1-102003524-C-G

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 0.449 in 152,012 control chromosomes in the GnomAD database, including 15,729 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 0.45 (15729 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.184

ACMG classification

Verdict is Benign. Variant got -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 = 0.55 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68186 AN: 151894 Hom.: 15730 Cov.: 32

Gnomad AFR AF: 0.395

Gnomad AMI AF: 0.436

Gnomad AMR AF: 0.534

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.568

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.281

Gnomad MID AF: 0.576

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.530

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

GnomAD4 genome AF: 0.449 AC: 68208 AN: 152012 Hom.: 15729 Cov.: 32 AF XY: 0.443 AC XY: 32917 AN XY: 74314

Gnomad4 AFR AF: 0.394

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.567

Gnomad4 SAS AF: 0.454

Gnomad4 FIN AF: 0.281

Gnomad4 NFE AF: 0.468

Gnomad4 OTH AF: 0.529

Alfa AF: 0.455 Hom.: 2737

Bravo AF: 0.465

Asia WGS AF: 0.508 AC: 1762 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.4
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6688672; hg19: chr1-102469080;