chr21-38777718-G-A

Variant names:

• chr21-38777718-G-A
• rs1209912
• ENST00000785403.1:n.448+1459G>A

Variant summary

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

The ENST00000785403.1(ENSG00000302272):​n.448+1459G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.551 in 152,004 control chromosomes in the GnomAD database, including 26,926 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 0.55 (26926 hom., cov: 32)
• Consequence: ENSG00000302272 ENST00000785403.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.553
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.7 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.448+1459G>A		intron	N/A
	ENSG00000302272	ENST00000785404.1		n.307-8639G>A		intron	N/A
	ENSG00000302272	ENST00000785405.1		n.234+1459G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83768 AN: 151884 Hom.: 26930 Cov.: 32

Gnomad AFR AF: 0.200

Gnomad AMI AF: 0.701

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.514

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.705

Gnomad OTH AF: 0.565

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

GnomAD4 genome AF: 0.551 AC: 83769 AN: 152004 Hom.: 26926 Cov.: 32 AF XY: 0.556 AC XY: 41296 AN XY: 74318

African (AFR) AF: 0.199 AC: 8263 AN: 41442

American (AMR) AF: 0.649 AC: 9910 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.660 AC: 2291 AN: 3470

East Asian (EAS) AF: 0.513 AC: 2647 AN: 5156

South Asian (SAS) AF: 0.577 AC: 2779 AN: 4814

European-Finnish (FIN) AF: 0.750 AC: 7926 AN: 10572

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.705 AC: 47948 AN: 67970

Other (OTH) AF: 0.564 AC: 1192 AN: 2112

Alfa AF: 0.610 Hom.: 9324

Bravo AF: 0.529

Asia WGS AF: 0.529 AC: 1843 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.61
PhyloP100		-0.55

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: rs1209912;

hg19: chr21-40149642;