rs6724689

Variant names:

• chr2-228360409-C-T
• rs6724689

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 0.185 in 151,972 control chromosomes in the GnomAD database, including 3,063 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 0.18 (3063 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.671

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 (AFR) allele frequency at 95% confidence interval = 0.292 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: 0.185 AC: 28062 AN: 151856 Hom.: 3055 Cov.: 32

Gnomad AFR AF: 0.297

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.153

Gnomad ASJ AF: 0.0865

Gnomad EAS AF: 0.127

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.191

Gnomad MID AF: 0.178

Gnomad NFE AF: 0.138

Gnomad OTH AF: 0.165

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

GnomAD4 genome AF: 0.185 AC: 28100 AN: 151972 Hom.: 3063 Cov.: 32 AF XY: 0.186 AC XY: 13796 AN XY: 74268

Gnomad4 AFR AF: 0.297

Gnomad4 AMR AF: 0.153

Gnomad4 ASJ AF: 0.0865

Gnomad4 EAS AF: 0.127

Gnomad4 SAS AF: 0.142

Gnomad4 FIN AF: 0.191

Gnomad4 NFE AF: 0.138

Gnomad4 OTH AF: 0.165

Alfa AF: 0.169 Hom.: 282

Bravo AF: 0.185

Asia WGS AF: 0.136 AC: 472 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.0
DANN	Benign	0.28

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6724689; hg19: chr2-229225125;