4-12320045-C-G

Variant names:

• chr4-12320045-C-G
• rs961996

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 0.438 in 151,872 control chromosomes in the GnomAD database, including 15,589 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 0.44 (15589 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800
• Publications: 2 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 (EAS) allele frequency at 95% confidence interval = 0.784 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: 0.438 AC: 66498 AN: 151754 Hom.: 15586 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.576

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.484

Gnomad EAS AF: 0.805

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.471

Gnomad OTH AF: 0.485

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

GnomAD4 genome AF: 0.438 AC: 66518 AN: 151872 Hom.: 15589 Cov.: 32 AF XY: 0.444 AC XY: 32987 AN XY: 74222

African (AFR) AF: 0.276 AC: 11440 AN: 41462

American (AMR) AF: 0.532 AC: 8114 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.484 AC: 1678 AN: 3468

East Asian (EAS) AF: 0.804 AC: 4122 AN: 5124

South Asian (SAS) AF: 0.528 AC: 2546 AN: 4818

European-Finnish (FIN) AF: 0.470 AC: 4963 AN: 10566

Middle Eastern (MID) AF: 0.558 AC: 164 AN: 294

European-Non Finnish (NFE) AF: 0.471 AC: 31951 AN: 67878

Other (OTH) AF: 0.482 AC: 1016 AN: 2110

Alfa AF: 0.320 Hom.: 982

Bravo AF: 0.440

Asia WGS AF: 0.589 AC: 2047 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	0.76
DANN	Benign	0.27
PhyloP100		-0.0080

Splicing

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

Other links and lift over

dbSNP: rs961996; hg19: chr4-12321669;