rs6688672

Variant names:

• chr1-102003524-C-A
• rs6688672

Your query was ambiguous. Multiple possible variants found:

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

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 0.449 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
• Publications: 3 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 = 0.55 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: 0.449 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

African (AFR) AF: 0.394 AC: 16335 AN: 41442

American (AMR) AF: 0.533 AC: 8154 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2144 AN: 3470

East Asian (EAS) AF: 0.567 AC: 2925 AN: 5158

South Asian (SAS) AF: 0.454 AC: 2192 AN: 4828

European-Finnish (FIN) AF: 0.281 AC: 2967 AN: 10572

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

European-Non Finnish (NFE) AF: 0.468 AC: 31806 AN: 67944

Other (OTH) AF: 0.529 AC: 1117 AN: 2110

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
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs6688672; hg19: chr1-102469080;