21-38785357-T-C

Variant names:

• chr21-38785357-T-C
• rs1209927
• ENST00000785403.1:n.449-1000T>C

Variant summary

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

The ENST00000785403.1(ENSG00000302272):​n.449-1000T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.696 in 152,172 control chromosomes in the GnomAD database, including 37,149 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 0.70 (37149 hom., cov: 33)
• Consequence: ENSG00000302272 ENST00000785403.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 1 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.717 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985480	XR_001755102.2	n.41-1000T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000302272	ENST00000785403.1	n.449-1000T>C		intron_variant	Intron 3 of 3
ENSG00000302272	ENST00000785404.1	n.307-1000T>C		intron_variant	Intron 2 of 2
ENSG00000302272	ENST00000785405.1	n.357-1000T>C		intron_variant	Intron 3 of 3
ENSG00000302272	ENST00000785410.1	n.152+428T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.696 AC: 105824 AN: 152054 Hom.: 37124 Cov.: 33

Gnomad AFR AF: 0.657

Gnomad AMI AF: 0.741

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.512

Gnomad SAS AF: 0.636

Gnomad FIN AF: 0.756

Gnomad MID AF: 0.728

Gnomad NFE AF: 0.723

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.696 AC: 105907 AN: 152172 Hom.: 37149 Cov.: 33 AF XY: 0.694 AC XY: 51655 AN XY: 74396

African (AFR) AF: 0.657 AC: 27297 AN: 41520

American (AMR) AF: 0.723 AC: 11051 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 2393 AN: 3472

East Asian (EAS) AF: 0.512 AC: 2649 AN: 5176

South Asian (SAS) AF: 0.635 AC: 3062 AN: 4822

European-Finnish (FIN) AF: 0.756 AC: 8006 AN: 10590

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.723 AC: 49120 AN: 67982

Other (OTH) AF: 0.681 AC: 1439 AN: 2112

Alfa AF: 0.710 Hom.: 145024

Bravo AF: 0.692

Asia WGS AF: 0.598 AC: 2084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.24
DANN	Benign	0.25
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1209927; hg19: chr21-40157281;