rs6024437

Variant names:

• chr20-55805499-C-T
• rs6024437
• XR_936887.2:n.83+1517C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_936887.2(LOC105372677):​n.83+1517C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.265 in 152,106 control chromosomes in the GnomAD database, including 6,525 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 0.27 (6525 hom., cov: 33)
• Consequence: LOC105372677 XR_936887.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.338
• Publications: 5 publications found

Genes affected

LOC105372677 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372677	XR_936887.2	n.83+1517C>T		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.265 AC: 40313 AN: 151988 Hom.: 6513 Cov.: 33

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.179

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.289

Gnomad EAS AF: 0.137

Gnomad SAS AF: 0.227

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.193

Gnomad OTH AF: 0.253

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

GnomAD4 genome AF: 0.265 AC: 40350 AN: 152106 Hom.: 6525 Cov.: 33 AF XY: 0.264 AC XY: 19599 AN XY: 74352

African (AFR) AF: 0.455 AC: 18880 AN: 41494

American (AMR) AF: 0.178 AC: 2710 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.289 AC: 1004 AN: 3472

East Asian (EAS) AF: 0.138 AC: 712 AN: 5172

South Asian (SAS) AF: 0.227 AC: 1094 AN: 4828

European-Finnish (FIN) AF: 0.190 AC: 2010 AN: 10586

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.193 AC: 13151 AN: 67968

Other (OTH) AF: 0.250 AC: 529 AN: 2116

Alfa AF: 0.214 Hom.: 16571

Bravo AF: 0.271

Asia WGS AF: 0.197 AC: 684 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	16
DANN	Benign	0.58
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs6024437; hg19: chr20-54380555;