rs1209926

Variant names:

• chr21-38785200-T-C
• rs1209926
• ENST00000785403.1:n.449-1157T>C

Variant summary

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

The ENST00000785403.1(ENSG00000302272):​n.449-1157T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.657 in 152,162 control chromosomes in the GnomAD database, including 33,320 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 0.66 (33320 hom., cov: 33)
• Consequence: ENSG00000302272 ENST00000785403.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511
• Publications: 4 publications found

Genes affected

ENSG00000302272 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.702 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985480	XR_001755102.2	n.40+1109T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302272	ENST00000785403.1	n.449-1157T>C		intron_variant	Intron 3 of 3
ENSG00000302272	ENST00000785404.1	n.307-1157T>C		intron_variant	Intron 2 of 2
ENSG00000302272	ENST00000785405.1	n.356+1109T>C		intron_variant	Intron 3 of 3
ENSG00000302272	ENST00000785410.1	n.152+271T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.657 AC: 99865 AN: 152044 Hom.: 33302 Cov.: 33

Gnomad AFR AF: 0.559

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.698

Gnomad ASJ AF: 0.669

Gnomad EAS AF: 0.509

Gnomad SAS AF: 0.596

Gnomad FIN AF: 0.753

Gnomad MID AF: 0.658

Gnomad NFE AF: 0.707

Gnomad OTH AF: 0.640

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

GnomAD4 genome AF: 0.657 AC: 99938 AN: 152162 Hom.: 33320 Cov.: 33 AF XY: 0.657 AC XY: 48841 AN XY: 74388

African (AFR) AF: 0.559 AC: 23208 AN: 41512

American (AMR) AF: 0.698 AC: 10675 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.669 AC: 2322 AN: 3472

East Asian (EAS) AF: 0.509 AC: 2634 AN: 5170

South Asian (SAS) AF: 0.595 AC: 2870 AN: 4826

European-Finnish (FIN) AF: 0.753 AC: 7979 AN: 10592

Middle Eastern (MID) AF: 0.660 AC: 194 AN: 294

European-Non Finnish (NFE) AF: 0.707 AC: 48068 AN: 67982

Other (OTH) AF: 0.639 AC: 1349 AN: 2110

Alfa AF: 0.686 Hom.: 36053

Bravo AF: 0.649

Asia WGS AF: 0.570 AC: 1987 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.1
DANN	Benign	0.64
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs1209926; hg19: chr21-40157124;