4-10124515-A-G

Position:

• chr4-10124515-A-G

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 0.445 in 152,074 control chromosomes in the GnomAD database, including 15,384 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 0.45 (15384 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.201

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.445 AC: 67647 AN: 151956 Hom.: 15366 Cov.: 33

Gnomad AFR AF: 0.354

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.539

Gnomad ASJ AF: 0.475

Gnomad EAS AF: 0.499

Gnomad SAS AF: 0.403

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.444

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

GnomAD4 genome AF: 0.445 AC: 67698 AN: 152074 Hom.: 15384 Cov.: 33 AF XY: 0.448 AC XY: 33272 AN XY: 74334

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.539

Gnomad4 ASJ AF: 0.475

Gnomad4 EAS AF: 0.499

Gnomad4 SAS AF: 0.403

Gnomad4 FIN AF: 0.470

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.445

Alfa AF: 0.467 Hom.: 2804

Bravo AF: 0.445

Asia WGS AF: 0.437 AC: 1523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.8
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11722989; hg19: chr4-10126139;