rs6825454

Variant names:

• chr4-154580036-T-C
• rs6825454

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 0.257 in 151,866 control chromosomes in the GnomAD database, including 5,193 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 0.26 (5193 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.426
• Publications: 17 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 = 0.425 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: 0.257 AC: 39023 AN: 151748 Hom.: 5191 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.255

Gnomad AMR AF: 0.235

Gnomad ASJ AF: 0.169

Gnomad EAS AF: 0.440

Gnomad SAS AF: 0.301

Gnomad FIN AF: 0.312

Gnomad MID AF: 0.199

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.257 AC: 39036 AN: 151866 Hom.: 5193 Cov.: 32 AF XY: 0.259 AC XY: 19240 AN XY: 74184

African (AFR) AF: 0.233 AC: 9668 AN: 41414

American (AMR) AF: 0.234 AC: 3572 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.169 AC: 586 AN: 3470

East Asian (EAS) AF: 0.440 AC: 2257 AN: 5128

South Asian (SAS) AF: 0.302 AC: 1454 AN: 4814

European-Finnish (FIN) AF: 0.312 AC: 3292 AN: 10536

Middle Eastern (MID) AF: 0.194 AC: 57 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17438 AN: 67934

Other (OTH) AF: 0.227 AC: 479 AN: 2110

Alfa AF: 0.258 Hom.: 8631

Bravo AF: 0.252

Asia WGS AF: 0.315 AC: 1091 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	2.7
DANN	Benign	0.58
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs6825454; hg19: chr4-155501188;