21-41099701-A-G

Variant names:

• chr21-41099701-A-G
• rs16998084
• ENST00000760344.1:n.187+13191T>C

Variant summary

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

The ENST00000760344.1(ENSG00000299081):​n.187+13191T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0615 in 152,278 control chromosomes in the GnomAD database, including 716 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 0.061 (716 hom., cov: 33)
• Consequence: ENSG00000299081 ENST00000760344.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.168
• Publications: 2 publications found

Genes affected

ENSG00000299081 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.175 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
ENSG00000299081	ENST00000760344.1	n.187+13191T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0614 AC: 9349 AN: 152160 Hom.: 715 Cov.: 33

Gnomad AFR AF: 0.179

Gnomad AMI AF: 0.0252

Gnomad AMR AF: 0.0424

Gnomad ASJ AF: 0.0285

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00207

Gnomad FIN AF: 0.0156

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0130

Gnomad OTH AF: 0.0492

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

GnomAD4 genome AF: 0.0615 AC: 9364 AN: 152278 Hom.: 716 Cov.: 33 AF XY: 0.0592 AC XY: 4408 AN XY: 74460

African (AFR) AF: 0.179 AC: 7417 AN: 41540

American (AMR) AF: 0.0425 AC: 651 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0285 AC: 99 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5192

South Asian (SAS) AF: 0.00207 AC: 10 AN: 4820

European-Finnish (FIN) AF: 0.0156 AC: 166 AN: 10608

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0130 AC: 883 AN: 68026

Other (OTH) AF: 0.0482 AC: 102 AN: 2114

Alfa AF: 0.0314 Hom.: 709

Bravo AF: 0.0683

Asia WGS AF: 0.00982 AC: 34 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	0.58
DANN	Benign	0.84
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs16998084; hg19: chr21-42471628;