rs6024454

Variant names:

• chr20-55818377-C-T
• rs6024454
• XR_936887.2:n.84-8382C>T

Variant summary

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

The XR_936887.2(LOC105372677):​n.84-8382C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.325 in 152,018 control chromosomes in the GnomAD database, including 11,069 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 0.33 (11069 hom., cov: 32)
• Consequence: LOC105372677 XR_936887.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.538
• Publications: 1 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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.638 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372677	XR_936887.2	n.84-8382C>T		intron_variant	Intron 1 of 2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49385 AN: 151900 Hom.: 11039 Cov.: 32

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.180

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.150

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.348

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.303

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

GnomAD4 genome AF: 0.325 AC: 49460 AN: 152018 Hom.: 11069 Cov.: 32 AF XY: 0.321 AC XY: 23814 AN XY: 74294

African (AFR) AF: 0.644 AC: 26699 AN: 41446

American (AMR) AF: 0.207 AC: 3163 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1056 AN: 3464

East Asian (EAS) AF: 0.151 AC: 779 AN: 5172

South Asian (SAS) AF: 0.233 AC: 1120 AN: 4816

European-Finnish (FIN) AF: 0.201 AC: 2125 AN: 10568

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13618 AN: 67962

Other (OTH) AF: 0.300 AC: 634 AN: 2112

Alfa AF: 0.237 Hom.: 3776

Bravo AF: 0.338

Asia WGS AF: 0.222 AC: 772 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.91
DANN	Benign	0.66
PhyloP100		-0.54

Splicing

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

Other links and lift over

dbSNP: rs6024454; hg19: chr20-54393433;