chr4-27077228-C-T

Variant names:

• chr4-27077228-C-T
• rs719575

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 0.331 in 151,836 control chromosomes in the GnomAD database, including 8,716 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 0.33 (8716 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.414
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.39 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: 0.331 AC: 50169 AN: 151718 Hom.: 8711 Cov.: 32

Gnomad AFR AF: 0.245

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.340

Gnomad ASJ AF: 0.327

Gnomad EAS AF: 0.117

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.370

Gnomad MID AF: 0.415

Gnomad NFE AF: 0.394

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.331 AC: 50183 AN: 151836 Hom.: 8716 Cov.: 32 AF XY: 0.326 AC XY: 24173 AN XY: 74206

African (AFR) AF: 0.245 AC: 10144 AN: 41400

American (AMR) AF: 0.340 AC: 5184 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.327 AC: 1134 AN: 3470

East Asian (EAS) AF: 0.117 AC: 606 AN: 5166

South Asian (SAS) AF: 0.310 AC: 1489 AN: 4802

European-Finnish (FIN) AF: 0.370 AC: 3881 AN: 10490

Middle Eastern (MID) AF: 0.412 AC: 121 AN: 294

European-Non Finnish (NFE) AF: 0.394 AC: 26761 AN: 67952

Other (OTH) AF: 0.301 AC: 633 AN: 2102

Alfa AF: 0.360 Hom.: 7400

Bravo AF: 0.321

Asia WGS AF: 0.225 AC: 781 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.9
DANN	Benign	0.78
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs719575; hg19: chr4-27078850;