rs11717948

Positions:

• chr3-183591640-G-A
• chr3-183591640-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0287 in 152,178 control chromosomes in the GnomAD database, including 84 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 0.029 (84 hom., cov: 32)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.235

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0287 (4371/152178) while in subpopulation NFE AF= 0.0392 (2663/67998). AF 95% confidence interval is 0.0379. There are 84 homozygotes in gnomad4. There are 2029 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 84 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.183591640G>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0288 AC: 4376 AN: 152060 Hom.: 85 Cov.: 32

Gnomad AFR AF: 0.00845

Gnomad AMI AF: 0.0549

Gnomad AMR AF: 0.0340

Gnomad ASJ AF: 0.0903

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0216

Gnomad FIN AF: 0.0249

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.0392

Gnomad OTH AF: 0.0374

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

GnomAD4 genome AF: 0.0287 AC: 4371 AN: 152178 Hom.: 84 Cov.: 32 AF XY: 0.0273 AC XY: 2029 AN XY: 74390

Gnomad4 AFR AF: 0.00843

Gnomad4 AMR AF: 0.0340

Gnomad4 ASJ AF: 0.0903

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0214

Gnomad4 FIN AF: 0.0249

Gnomad4 NFE AF: 0.0392

Gnomad4 OTH AF: 0.0370

Alfa AF: 0.0211 Hom.: 14

Bravo AF: 0.0293

Asia WGS AF: 0.0110 AC: 37 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.3
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11717948; hg19: chr3-183309428;