4-22019877-C-T

Variant names:

• chr4-22019877-C-T
• rs16872248
• ENST00000510705.3:n.446-39207C>T

Variant summary

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

The ENST00000510705.3(ENSG00000250039):​n.446-39207C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,080 control chromosomes in the GnomAD database, including 2,447 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 0.11 (2447 hom., cov: 33)
• Consequence: ENSG00000250039 ENST00000510705.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229

Genes affected

ENSG00000250039 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000250039	ENST00000510705.3	n.446-39207C>T		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16551 AN: 151962 Hom.: 2446 Cov.: 33

Gnomad AFR AF: 0.340

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0484

Gnomad ASJ AF: 0.0406

Gnomad EAS AF: 0.0470

Gnomad SAS AF: 0.0315

Gnomad FIN AF: 0.00208

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0145

Gnomad OTH AF: 0.0876

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

GnomAD4 genome AF: 0.109 AC: 16581 AN: 152080 Hom.: 2447 Cov.: 33 AF XY: 0.105 AC XY: 7837 AN XY: 74362

Gnomad4 AFR AF: 0.340

Gnomad4 AMR AF: 0.0483

Gnomad4 ASJ AF: 0.0406

Gnomad4 EAS AF: 0.0469

Gnomad4 SAS AF: 0.0313

Gnomad4 FIN AF: 0.00208

Gnomad4 NFE AF: 0.0145

Gnomad4 OTH AF: 0.0867

Alfa AF: 0.0392 Hom.: 485

Bravo AF: 0.123

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.9
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16872248; hg19: chr4-22021500;