21-41290332-C-T

Variant names:

• chr21-41290332-C-T
• rs9984207
• ENST00000754075.1:n.445+3197G>A

Variant summary

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

The ENST00000754075.1(ENSG00000298244):​n.445+3197G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.441 in 146,776 control chromosomes in the GnomAD database, including 14,038 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 0.44 (14038 hom., cov: 31)
• Consequence: ENSG00000298244 ENST00000754075.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100
• Publications: 4 publications found

Genes affected

ENSG00000298244 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.597 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
ENSG00000298244	ENST00000754075.1	n.445+3197G>A		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.441 AC: 64702 AN: 146660 Hom.: 14029 Cov.: 31

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.372

Gnomad AMR AF: 0.373

Gnomad ASJ AF: 0.412

Gnomad EAS AF: 0.585

Gnomad SAS AF: 0.616

Gnomad FIN AF: 0.397

Gnomad MID AF: 0.393

Gnomad NFE AF: 0.417

Gnomad OTH AF: 0.456

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

GnomAD4 genome AF: 0.441 AC: 64736 AN: 146776 Hom.: 14038 Cov.: 31 AF XY: 0.445 AC XY: 31808 AN XY: 71530

African (AFR) AF: 0.483 AC: 19199 AN: 39728

American (AMR) AF: 0.372 AC: 5375 AN: 14436

Ashkenazi Jewish (ASJ) AF: 0.412 AC: 1398 AN: 3394

East Asian (EAS) AF: 0.585 AC: 2947 AN: 5034

South Asian (SAS) AF: 0.616 AC: 2844 AN: 4618

European-Finnish (FIN) AF: 0.397 AC: 3979 AN: 10018

Middle Eastern (MID) AF: 0.394 AC: 108 AN: 274

European-Non Finnish (NFE) AF: 0.417 AC: 27640 AN: 66362

Other (OTH) AF: 0.452 AC: 914 AN: 2020

Alfa AF: 0.413 Hom.: 16074

Bravo AF: 0.421

Asia WGS AF: 0.542 AC: 1883 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.3
DANN	Benign	0.81
PhyloP100		0.0010

Splicing

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

Other links and lift over

dbSNP: rs9984207; hg19: chr21-42662259;