chr4-126746789-A-G

Variant names:

• chr4-126746789-A-G
• rs951784

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 0.201 in 151,846 control chromosomes in the GnomAD database, including 3,748 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 0.20 (3748 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.355 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: 0.201 AC: 30491 AN: 151730 Hom.: 3746 Cov.: 32

Gnomad AFR AF: 0.0909

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.227

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.335

Gnomad FIN AF: 0.236

Gnomad MID AF: 0.309

Gnomad NFE AF: 0.210

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.201 AC: 30504 AN: 151846 Hom.: 3748 Cov.: 32 AF XY: 0.210 AC XY: 15588 AN XY: 74216

African (AFR) AF: 0.0908 AC: 3768 AN: 41514

American (AMR) AF: 0.363 AC: 5531 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.227 AC: 786 AN: 3468

East Asian (EAS) AF: 0.267 AC: 1383 AN: 5182

South Asian (SAS) AF: 0.333 AC: 1605 AN: 4816

European-Finnish (FIN) AF: 0.236 AC: 2491 AN: 10550

Middle Eastern (MID) AF: 0.318 AC: 93 AN: 292

European-Non Finnish (NFE) AF: 0.210 AC: 14197 AN: 67750

Other (OTH) AF: 0.226 AC: 476 AN: 2108

Alfa AF: 0.215 Hom.: 1995

Bravo AF: 0.208

Asia WGS AF: 0.284 AC: 988 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.2
DANN	Benign	0.64
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs951784; hg19: chr4-127667944;