rs7281733

Variant names:

• chr21-41283588-G-A
• rs7281733
• ENST00000754075.1:n.446-972C>T

Your query was ambiguous. Multiple possible variants found:

• chr21-41283588-G-A
• chr21-41283588-G-C

Variant summary

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

The ENST00000754075.1(ENSG00000298244):​n.446-972C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.221 in 152,100 control chromosomes in the GnomAD database, including 4,432 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 0.22 (4432 hom., cov: 32)
• Consequence: ENSG00000298244 ENST00000754075.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 5 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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.373 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.446-972C>T		intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes AF: 0.221 AC: 33537 AN: 151982 Hom.: 4417 Cov.: 32

Gnomad AFR AF: 0.378

Gnomad AMI AF: 0.0965

Gnomad AMR AF: 0.216

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.152

Gnomad SAS AF: 0.247

Gnomad FIN AF: 0.159

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.142

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.221 AC: 33606 AN: 152100 Hom.: 4432 Cov.: 32 AF XY: 0.222 AC XY: 16508 AN XY: 74372

African (AFR) AF: 0.378 AC: 15679 AN: 41468

American (AMR) AF: 0.216 AC: 3297 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 673 AN: 3468

East Asian (EAS) AF: 0.152 AC: 785 AN: 5174

South Asian (SAS) AF: 0.247 AC: 1190 AN: 4824

European-Finnish (FIN) AF: 0.159 AC: 1683 AN: 10580

Middle Eastern (MID) AF: 0.248 AC: 73 AN: 294

European-Non Finnish (NFE) AF: 0.142 AC: 9662 AN: 67996

Other (OTH) AF: 0.226 AC: 476 AN: 2110

Alfa AF: 0.172 Hom.: 7766

Bravo AF: 0.229

Asia WGS AF: 0.258 AC: 900 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.54
DANN	Benign	0.40
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs7281733; hg19: chr21-42655515;