rs6024460

Variant names:

• chr20-55820485-A-G
• rs6024460
• XR_936887.2:n.84-6274A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_936887.2(LOC105372677):​n.84-6274A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 151,934 control chromosomes in the GnomAD database, including 5,174 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 0.24 (5174 hom., cov: 31)
• Consequence: LOC105372677 XR_936887.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.72
• Publications: 4 publications found

Genes affected

LOC105372677 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372677	XR_936887.2	n.84-6274A>G		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.244 AC: 36973 AN: 151816 Hom.: 5163 Cov.: 31

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.168

Gnomad ASJ AF: 0.291

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.226

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.333

Gnomad NFE AF: 0.192

Gnomad OTH AF: 0.242

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

GnomAD4 genome AF: 0.244 AC: 37002 AN: 151934 Hom.: 5174 Cov.: 31 AF XY: 0.243 AC XY: 18042 AN XY: 74278

African (AFR) AF: 0.382 AC: 15826 AN: 41398

American (AMR) AF: 0.168 AC: 2566 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.291 AC: 1009 AN: 3470

East Asian (EAS) AF: 0.138 AC: 712 AN: 5158

South Asian (SAS) AF: 0.226 AC: 1088 AN: 4812

European-Finnish (FIN) AF: 0.187 AC: 1970 AN: 10546

Middle Eastern (MID) AF: 0.331 AC: 96 AN: 290

European-Non Finnish (NFE) AF: 0.192 AC: 13064 AN: 67974

Other (OTH) AF: 0.240 AC: 506 AN: 2112

Alfa AF: 0.210 Hom.: 5893

Bravo AF: 0.246

Asia WGS AF: 0.194 AC: 671 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.025
DANN	Benign	0.58
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs6024460; hg19: chr20-54395541;