rs1999316

Variant names:

• chr21-28480782-A-G
• rs1999316
• ENST00000430247.1:n.239+2175T>C

Your query was ambiguous. Multiple possible variants found:

• chr21-28480782-A-G
• chr21-28480782-A-T

Variant summary

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

The ENST00000430247.1(ENSG00000232855):​n.239+2175T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 152,094 control chromosomes in the GnomAD database, including 33,113 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 0.65 (33113 hom., cov: 32)
• Consequence: ENSG00000232855 ENST00000430247.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• Publications: 1 publications found

Genes affected

ENSG00000232855 (HGNC:58104):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.748 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
ENSG00000232855	ENST00000430247.1	n.239+2175T>C		intron_variant	Intron 3 of 4	5
ENSG00000232855	ENST00000433310.6	n.457-34310T>C		intron_variant	Intron 3 of 4	2
ENSG00000232855	ENST00000654020.1	n.137+4810T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.646 AC: 98144 AN: 151974 Hom.: 33098 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.700

Gnomad EAS AF: 0.262

Gnomad SAS AF: 0.635

Gnomad FIN AF: 0.774

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.754

Gnomad OTH AF: 0.663

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

GnomAD4 genome AF: 0.646 AC: 98193 AN: 152094 Hom.: 33113 Cov.: 32 AF XY: 0.643 AC XY: 47778 AN XY: 74350

African (AFR) AF: 0.509 AC: 21085 AN: 41456

American (AMR) AF: 0.562 AC: 8587 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.700 AC: 2429 AN: 3470

East Asian (EAS) AF: 0.262 AC: 1354 AN: 5166

South Asian (SAS) AF: 0.636 AC: 3067 AN: 4822

European-Finnish (FIN) AF: 0.774 AC: 8197 AN: 10588

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.754 AC: 51241 AN: 68002

Other (OTH) AF: 0.662 AC: 1401 AN: 2116

Alfa AF: 0.716 Hom.: 63718

Bravo AF: 0.621

Asia WGS AF: 0.449 AC: 1566 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.87
DANN	Benign	0.59
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1999316; hg19: chr21-29853103;