4-27450860-G-T

Variant names:

• chr4-27450860-G-T
• rs10489018

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 0.216 in 152,054 control chromosomes in the GnomAD database, including 4,428 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 0.22 (4428 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.01
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.302 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: 0.216 AC: 32842 AN: 151936 Hom.: 4427 Cov.: 32

Gnomad AFR AF: 0.0887

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.268

Gnomad EAS AF: 0.00578

Gnomad SAS AF: 0.229

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.306

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.216 AC: 32831 AN: 152054 Hom.: 4428 Cov.: 32 AF XY: 0.210 AC XY: 15617 AN XY: 74298

African (AFR) AF: 0.0885 AC: 3675 AN: 41534

American (AMR) AF: 0.169 AC: 2572 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.268 AC: 931 AN: 3470

East Asian (EAS) AF: 0.00579 AC: 30 AN: 5178

South Asian (SAS) AF: 0.229 AC: 1100 AN: 4808

European-Finnish (FIN) AF: 0.290 AC: 3067 AN: 10576

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

European-Non Finnish (NFE) AF: 0.306 AC: 20778 AN: 67906

Other (OTH) AF: 0.203 AC: 429 AN: 2112

Alfa AF: 0.273 Hom.: 5493

Bravo AF: 0.199

Asia WGS AF: 0.0940 AC: 326 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.023
DANN	Benign	0.26
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10489018; hg19: chr4-27452482;