rs11939979

Variant names:

• chr4-145567175-A-C
• rs11939979

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 0.504 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
• Publications: 6 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.586 AC: 24204 AN: 41296

American (AMR) AF: 0.376 AC: 5730 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1449 AN: 3472

East Asian (EAS) AF: 0.275 AC: 1417 AN: 5152

South Asian (SAS) AF: 0.532 AC: 2556 AN: 4804

European-Finnish (FIN) AF: 0.481 AC: 5046 AN: 10490

Middle Eastern (MID) AF: 0.397 AC: 116 AN: 292

European-Non Finnish (NFE) AF: 0.509 AC: 34543 AN: 67878

Other (OTH) AF: 0.478 AC: 1007 AN: 2106

Alfa AF: 0.503 Hom.: 82162

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
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs11939979; hg19: chr4-146488327;