rs2728127

chr4-87973963-A-Gchr4-87973963-A-T

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 0.368 in 152,140 control chromosomes in the GnomAD database, including 11,252 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 0.37 (11252 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55933 AN: 152022 Hom.: 11228 Cov.: 33

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.365

Gnomad SAS AF: 0.255

Gnomad FIN AF: 0.365

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.355

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

GnomAD4 genome AF: 0.368 AC: 56002 AN: 152140 Hom.: 11252 Cov.: 33 AF XY: 0.368 AC XY: 27382 AN XY: 74402

Gnomad4 AFR AF: 0.535

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.364

Gnomad4 SAS AF: 0.256

Gnomad4 FIN AF: 0.365

Gnomad4 NFE AF: 0.298

Gnomad4 OTH AF: 0.355

Alfa AF: 0.322 Hom.: 3109

Bravo AF: 0.368

Asia WGS AF: 0.309 AC: 1074 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	9.3
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2728127; hg19: chr4-88895115;