rs11939979

chr4-145567175-A-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 0.504 in 151,630 control chromosomes in the GnomAD database, including 19,862 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 0.50 (19862 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.58 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: 0.504 AC: 76373 AN: 151512 Hom.: 19823 Cov.: 30

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.377

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.533

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.476

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

GnomAD4 genome AF: 0.504 AC: 76470 AN: 151630 Hom.: 19862 Cov.: 30 AF XY: 0.499 AC XY: 37009 AN XY: 74094

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.376

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.275

Gnomad4 SAS AF: 0.532

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.509

Gnomad4 OTH AF: 0.478

Alfa AF: 0.499 Hom.: 38196

Bravo AF: 0.497

Asia WGS AF: 0.458 AC: 1595 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.8
Dann	Benign	0.22

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11939979; hg19: chr4-146488327;