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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000785403.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302272	ENST00000785403.1		n.449-1157T>C		intron	N/A
	ENSG00000302272	ENST00000785404.1		n.307-1157T>C		intron	N/A
	ENSG00000302272	ENST00000785405.1		n.356+1109T>C		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1209926;

hg19: chr21-40157124;