rs1640923

Positions:

• chr16-11227120-A-G

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 0.198 in 152,058 control chromosomes in the GnomAD database, including 3,623 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 0.20 (3623 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.537

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.394 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.11227120A>G		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30068 AN: 151940 Hom.: 3601 Cov.: 30

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.268

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.163

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

GnomAD4 genome AF: 0.198 AC: 30124 AN: 152058 Hom.: 3623 Cov.: 30 AF XY: 0.203 AC XY: 15077 AN XY: 74320

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.306

Gnomad4 ASJ AF: 0.105

Gnomad4 EAS AF: 0.408

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.140

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.162

Alfa AF: 0.180 Hom.: 364

Bravo AF: 0.214

Asia WGS AF: 0.357 AC: 1243 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	2.5
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1640923; hg19: chr16-11320977;