rs2066854

Variant names:

• chr4-154614029-T-A
• rs2066854

Your query was ambiguous. Multiple possible variants found:

• chr4-154614029-T-A
• chr4-154614029-T-G

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 0.256 in 151,992 control chromosomes in the GnomAD database, including 5,254 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 (5254 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.421
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.435 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: 0.256 AC: 38936 AN: 151874 Hom.: 5246 Cov.: 32

Gnomad AFR AF: 0.265

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.450

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.242

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.256 AC: 38974 AN: 151992 Hom.: 5254 Cov.: 32 AF XY: 0.259 AC XY: 19266 AN XY: 74290

African (AFR) AF: 0.266 AC: 11018 AN: 41478

American (AMR) AF: 0.217 AC: 3319 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 494 AN: 3470

East Asian (EAS) AF: 0.450 AC: 2317 AN: 5150

South Asian (SAS) AF: 0.294 AC: 1418 AN: 4816

European-Finnish (FIN) AF: 0.306 AC: 3229 AN: 10558

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.242 AC: 16436 AN: 67940

Other (OTH) AF: 0.220 AC: 465 AN: 2112

Alfa AF: 0.243 Hom.: 639

Bravo AF: 0.252

Asia WGS AF: 0.319 AC: 1107 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.50
PhyloP100		0.42

Splicing

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

Other links and lift over

dbSNP: rs2066854; hg19: chr4-155535181;