rs6024454

chr20-55818377-C-T

Variant summary

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

The XR_936887.2(LOC105372677):n.84-8382C>T variant causes a intron, non coding transcript 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, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.538

Genes affected

LOC105372677 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC105372677	XR_936887.2	n.84-8382C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.644

Gnomad4 AMR AF: 0.207

Gnomad4 ASJ AF: 0.305

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.233

Gnomad4 FIN AF: 0.201

Gnomad4 NFE AF: 0.200

Gnomad4 OTH AF: 0.300

Alfa AF: 0.233 Hom.: 2485

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6024454; hg19: chr20-54393433;