rs754284

Variant names:

• chr7-128931424-C-G
• rs754284

Your query was ambiguous. Multiple possible variants found:

• chr7-128931424-C-G
• chr7-128931424-C-T

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 0.279 in 152,086 control chromosomes in the GnomAD database, including 6,433 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 0.28 (6433 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142
• Publications: 3 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 = 0.323 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: 0.280 AC: 42493 AN: 151968 Hom.: 6432 Cov.: 32

Gnomad AFR AF: 0.199

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.279 AC: 42507 AN: 152086 Hom.: 6433 Cov.: 32 AF XY: 0.281 AC XY: 20905 AN XY: 74342

African (AFR) AF: 0.199 AC: 8251 AN: 41492

American (AMR) AF: 0.214 AC: 3270 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 960 AN: 3472

East Asian (EAS) AF: 0.310 AC: 1603 AN: 5174

South Asian (SAS) AF: 0.309 AC: 1487 AN: 4812

European-Finnish (FIN) AF: 0.354 AC: 3741 AN: 10578

Middle Eastern (MID) AF: 0.272 AC: 80 AN: 294

European-Non Finnish (NFE) AF: 0.327 AC: 22214 AN: 67958

Other (OTH) AF: 0.256 AC: 541 AN: 2116

Alfa AF: 0.172 Hom.: 355

Bravo AF: 0.266

Asia WGS AF: 0.304 AC: 1055 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	7.7
DANN	Benign	0.81
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs754284; hg19: chr7-128571478;