5-21114819-A-T

Variant names:

• chr5-21114819-A-T
• rs248208
• XR_001742406.2:n.124-973T>A

Variant summary

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

The XR_925839.3(LOC105374678):​n.214-973T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,134 control chromosomes in the GnomAD database, including 4,718 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 0.23 (4718 hom., cov: 33)
• Consequence: LOC105374678 XR_925839.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610

Genes affected

LOC105374678 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.555 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105374678	XR_001742406.2	n.124-973T>A		intron_variant	Intron 1 of 5
LOC105374678	XR_925839.3	n.214-973T>A		intron_variant	Intron 1 of 3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34268 AN: 152016 Hom.: 4708 Cov.: 33

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.432

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.397

Gnomad FIN AF: 0.269

Gnomad MID AF: 0.193

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.267

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

GnomAD4 genome AF: 0.225 AC: 34283 AN: 152134 Hom.: 4718 Cov.: 33 AF XY: 0.236 AC XY: 17508 AN XY: 74338

Gnomad4 AFR AF: 0.103

Gnomad4 AMR AF: 0.358

Gnomad4 ASJ AF: 0.198

Gnomad4 EAS AF: 0.572

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.269

Gnomad4 NFE AF: 0.222

Gnomad4 OTH AF: 0.271

Alfa AF: 0.220 Hom.: 490

Bravo AF: 0.228

Asia WGS AF: 0.515 AC: 1790 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.6
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs248208; hg19: chr5-21114928;