chr4-107389051-C-A

Variant names:

• chr4-107389051-C-A
• rs4956093

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 0.597 in 152,022 control chromosomes in the GnomAD database, including 27,081 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 0.60 (27081 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0850
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.606 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: 0.597 AC: 90729 AN: 151904 Hom.: 27075 Cov.: 32

Gnomad AFR AF: 0.582

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.625

Gnomad SAS AF: 0.608

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.597 AC: 90766 AN: 152022 Hom.: 27081 Cov.: 32 AF XY: 0.597 AC XY: 44360 AN XY: 74302

African (AFR) AF: 0.581 AC: 24100 AN: 41456

American (AMR) AF: 0.551 AC: 8413 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.601 AC: 2087 AN: 3470

East Asian (EAS) AF: 0.624 AC: 3216 AN: 5156

South Asian (SAS) AF: 0.607 AC: 2923 AN: 4814

European-Finnish (FIN) AF: 0.623 AC: 6579 AN: 10566

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.609 AC: 41402 AN: 67976

Other (OTH) AF: 0.615 AC: 1298 AN: 2110

Alfa AF: 0.523 Hom.: 2452

Bravo AF: 0.589

Asia WGS AF: 0.611 AC: 2128 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.5
DANN	Benign	0.56
PhyloP100		-0.085

Splicing

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

Other links and lift over

dbSNP: rs4956093; hg19: chr4-108310208;