rs6093416

Variant names:

• chr20-40986143-G-A
• rs6093416
• NR_145524.1:n.209+5222G>A

Your query was ambiguous. Multiple possible variants found:

• chr20-40986143-G-A
• chr20-40986143-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_145524.1(LOC100128988):​n.209+5222G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 151,952 control chromosomes in the GnomAD database, including 8,223 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 0.28 (8223 hom., cov: 32)
• Consequence: LOC100128988 NR_145524.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33

Genes affected

LOC100128988 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.529 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100128988	NR_145524.1	n.209+5222G>A		intron_variant	Intron 1 of 3
LOC100128988	NR_145525.1	n.209+5222G>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.277 AC: 42131 AN: 151834 Hom.: 8196 Cov.: 32

Gnomad AFR AF: 0.532

Gnomad AMI AF: 0.184

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.151

Gnomad EAS AF: 0.546

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.147

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.278 AC: 42202 AN: 151952 Hom.: 8223 Cov.: 32 AF XY: 0.280 AC XY: 20794 AN XY: 74298

Gnomad4 AFR AF: 0.532

Gnomad4 AMR AF: 0.299

Gnomad4 ASJ AF: 0.151

Gnomad4 EAS AF: 0.545

Gnomad4 SAS AF: 0.220

Gnomad4 FIN AF: 0.147

Gnomad4 NFE AF: 0.131

Gnomad4 OTH AF: 0.266

Alfa AF: 0.140 Hom.: 909

Bravo AF: 0.303

Asia WGS AF: 0.340 AC: 1183 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.011
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6093416; hg19: chr20-39614783;