5-21114819-A-T

Variant names:

• chr5-21114819-A-T
• rs248208
• ENST00000741983.1:n.211-973T>A

Variant summary

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

The ENST00000741983.1(ENSG00000296785):​n.211-973T>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: ENSG00000296785 ENST00000741983.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0610
• Publications: 1 publications found

Genes affected

ENSG00000296785 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000741983.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296785	ENST00000741983.1		n.211-973T>A		intron	N/A

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

African (AFR) AF: 0.103 AC: 4287 AN: 41530

American (AMR) AF: 0.358 AC: 5470 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 686 AN: 3468

East Asian (EAS) AF: 0.572 AC: 2958 AN: 5168

South Asian (SAS) AF: 0.396 AC: 1912 AN: 4826

European-Finnish (FIN) AF: 0.269 AC: 2843 AN: 10554

Middle Eastern (MID) AF: 0.190 AC: 56 AN: 294

European-Non Finnish (NFE) AF: 0.222 AC: 15105 AN: 67980

Other (OTH) AF: 0.271 AC: 572 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.6
DANN	Benign	0.35
PhyloP100		0.061

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs248208;

hg19: chr5-21114928;