rs2454275

Variant names:

• chr6-91838864-A-G
• rs2454275

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 0.186 in 151,990 control chromosomes in the GnomAD database, including 2,752 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 0.19 (2752 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.34

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.243 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: 0.186 AC: 28296 AN: 151872 Hom.: 2746 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.200

Gnomad SAS AF: 0.253

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.172

Gnomad OTH AF: 0.164

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

GnomAD4 genome AF: 0.186 AC: 28324 AN: 151990 Hom.: 2752 Cov.: 32 AF XY: 0.193 AC XY: 14302 AN XY: 74270

Gnomad4 AFR AF: 0.210

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.200

Gnomad4 SAS AF: 0.255

Gnomad4 FIN AF: 0.253

Gnomad4 NFE AF: 0.172

Gnomad4 OTH AF: 0.162

Alfa AF: 0.178 Hom.: 1325

Bravo AF: 0.176

Asia WGS AF: 0.206 AC: 717 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.8
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2454275; hg19: chr6-92548582;