rs961996

Positions:

• chr4-12320045-C-G
• chr4-12320045-C-T

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 0.438 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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00800

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
		n.12320045C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.532

Gnomad4 ASJ AF: 0.484

Gnomad4 EAS AF: 0.804

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.470

Gnomad4 NFE AF: 0.471

Gnomad4 OTH AF: 0.482

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs961996; hg19: chr4-12321669;