rs6547853

Variant names:

• chr2-28423934-G-A
• rs6547853

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 0.348 in 152,022 control chromosomes in the GnomAD database, including 9,739 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 0.35 (9739 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.821

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 (NFE) allele frequency at 95% confidence interval = 0.38 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: 0.348 AC: 52866 AN: 151904 Hom.: 9730 Cov.: 32

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.374

Gnomad AMR AF: 0.268

Gnomad ASJ AF: 0.377

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.179

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.348 AC: 52897 AN: 152022 Hom.: 9739 Cov.: 32 AF XY: 0.338 AC XY: 25155 AN XY: 74320

Gnomad4 AFR AF: 0.380

Gnomad4 AMR AF: 0.268

Gnomad4 ASJ AF: 0.377

Gnomad4 EAS AF: 0.0106

Gnomad4 SAS AF: 0.179

Gnomad4 FIN AF: 0.345

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.330

Alfa AF: 0.368 Hom.: 14126

Bravo AF: 0.342

Asia WGS AF: 0.129 AC: 451 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.8
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: rs6547853; hg19: chr2-28646801;