rs6547626

chr2-27423903-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 0.471 in 151,946 control chromosomes in the GnomAD database, including 18,613 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 0.47 (18613 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286

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 = 0.684 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: 0.471 AC: 71518 AN: 151828 Hom.: 18565 Cov.: 31

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.220

Gnomad AMR AF: 0.474

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.425

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.372

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.412

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

GnomAD4 genome AF: 0.471 AC: 71632 AN: 151946 Hom.: 18613 Cov.: 31 AF XY: 0.470 AC XY: 34896 AN XY: 74282

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.474

Gnomad4 ASJ AF: 0.334

Gnomad4 EAS AF: 0.154

Gnomad4 SAS AF: 0.426

Gnomad4 FIN AF: 0.430

Gnomad4 NFE AF: 0.383

Gnomad4 OTH AF: 0.416

Alfa AF: 0.441 Hom.: 2530

Bravo AF: 0.483

Asia WGS AF: 0.362 AC: 1258 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	1.8
Dann	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6547626; hg19: chr2-27646770;