rs4728142

Variant names:

• chr7-128933913-G-A
• rs4728142

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 0.377 in 152,036 control chromosomes in the GnomAD database, including 11,498 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 0.38 (11498 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.167
• Publications: 209 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 (NFE) allele frequency at 95% confidence interval = 0.437 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: 0.377 AC: 57261 AN: 151920 Hom.: 11502 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.458

Gnomad AMR AF: 0.393

Gnomad ASJ AF: 0.505

Gnomad EAS AF: 0.122

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.441

Gnomad OTH AF: 0.411

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

GnomAD4 genome AF: 0.377 AC: 57272 AN: 152036 Hom.: 11498 Cov.: 32 AF XY: 0.371 AC XY: 27601 AN XY: 74322

African (AFR) AF: 0.275 AC: 11415 AN: 41444

American (AMR) AF: 0.392 AC: 5997 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.505 AC: 1750 AN: 3466

East Asian (EAS) AF: 0.122 AC: 631 AN: 5176

South Asian (SAS) AF: 0.392 AC: 1886 AN: 4808

European-Finnish (FIN) AF: 0.396 AC: 4187 AN: 10564

Middle Eastern (MID) AF: 0.473 AC: 138 AN: 292

European-Non Finnish (NFE) AF: 0.441 AC: 29988 AN: 67970

Other (OTH) AF: 0.408 AC: 863 AN: 2114

Alfa AF: 0.419 Hom.: 55490

Bravo AF: 0.373

Asia WGS AF: 0.241 AC: 840 AN: 3478

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	0.41
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs4728142; hg19: chr7-128573967;