rs11945798

Positions:

• chr4-12767608-T-C

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 0.0852 in 151,844 control chromosomes in the GnomAD database, including 992 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 0.085 (992 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0890

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.201 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0850 AC: 12902 AN: 151708 Hom.: 990 Cov.: 32

Gnomad AFR AF: 0.204

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0568

Gnomad ASJ AF: 0.0320

Gnomad EAS AF: 0.0237

Gnomad SAS AF: 0.0640

Gnomad FIN AF: 0.0360

Gnomad MID AF: 0.0784

Gnomad NFE AF: 0.0363

Gnomad OTH AF: 0.0803

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

GnomAD4 genome AF: 0.0852 AC: 12932 AN: 151844 Hom.: 992 Cov.: 32 AF XY: 0.0835 AC XY: 6201 AN XY: 74234

Gnomad4 AFR AF: 0.204

Gnomad4 AMR AF: 0.0569

Gnomad4 ASJ AF: 0.0320

Gnomad4 EAS AF: 0.0242

Gnomad4 SAS AF: 0.0632

Gnomad4 FIN AF: 0.0360

Gnomad4 NFE AF: 0.0363

Gnomad4 OTH AF: 0.0796

Alfa AF: 0.0684 Hom.: 82

Bravo AF: 0.0915

Asia WGS AF: 0.0450 AC: 154 AN: 3428

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11945798; hg19: chr4-12769232;