ENST00000785194.1:n.221-4444C>T

Variant names:

• chr13-21809114-C-T
• rs672905
• ENST00000785194.1:n.221-4444C>T

Variant summary

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

The ENST00000785194.1(ENSG00000302249):​n.221-4444C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.388 in 152,104 control chromosomes in the GnomAD database, including 13,352 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 0.39 (13352 hom., cov: 33)
• Consequence: ENSG00000302249 ENST00000785194.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.339
• Publications: 1 publications found

Genes affected

ENSG00000302249 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903132	XR_007063714.1	n.216-4444C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302249	ENST00000785194.1	n.221-4444C>T		intron_variant	Intron 1 of 2
ENSG00000302249	ENST00000785195.1	n.236-4444C>T		intron_variant	Intron 1 of 2
ENSG00000302249	ENST00000785196.1	n.239-4444C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.388 AC: 59005 AN: 151986 Hom.: 13324 Cov.: 33

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.275

Gnomad ASJ AF: 0.315

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.234

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.388 AC: 59083 AN: 152104 Hom.: 13352 Cov.: 33 AF XY: 0.382 AC XY: 28407 AN XY: 74334

African (AFR) AF: 0.638 AC: 26486 AN: 41492

American (AMR) AF: 0.275 AC: 4210 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.315 AC: 1093 AN: 3470

East Asian (EAS) AF: 0.237 AC: 1229 AN: 5186

South Asian (SAS) AF: 0.235 AC: 1131 AN: 4816

European-Finnish (FIN) AF: 0.308 AC: 3245 AN: 10550

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20609 AN: 67988

Other (OTH) AF: 0.329 AC: 695 AN: 2114

Alfa AF: 0.300 Hom.: 2760

Bravo AF: 0.400

Asia WGS AF: 0.269 AC: 940 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.31
DANN	Benign	0.59
PhyloP100		-0.34

Splicing

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

Other links and lift over

dbSNP: rs672905; hg19: chr13-22383253;