chr21-31024249-G-A

Variant names:

• chr21-31024249-G-A
• rs11910746
• ENST00000726471.1:n.404-7383C>T

Variant summary

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

The ENST00000726471.1(ENSG00000294875):​n.404-7383C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.104 in 152,214 control chromosomes in the GnomAD database, including 1,312 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 0.10 (1312 hom., cov: 32)
• Consequence: ENSG00000294875 ENST00000726471.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.813
• Publications: 1 publications found

Genes affected

ENSG00000294875 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000726471.1. 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
	ENSG00000294875	ENST00000726471.1		n.404-7383C>T		intron	N/A
	ENSG00000294875	ENST00000726472.1		n.404-9481C>T		intron	N/A
	ENSG00000294875	ENST00000726473.1		n.334-9481C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15753 AN: 152096 Hom.: 1307 Cov.: 32

Gnomad AFR AF: 0.197

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.209

Gnomad ASJ AF: 0.0617

Gnomad EAS AF: 0.0635

Gnomad SAS AF: 0.0762

Gnomad FIN AF: 0.0357

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0422

Gnomad OTH AF: 0.0956

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

GnomAD4 genome AF: 0.104 AC: 15788 AN: 152214 Hom.: 1312 Cov.: 32 AF XY: 0.105 AC XY: 7835 AN XY: 74424

African (AFR) AF: 0.197 AC: 8183 AN: 41516

American (AMR) AF: 0.209 AC: 3202 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0617 AC: 214 AN: 3468

East Asian (EAS) AF: 0.0640 AC: 332 AN: 5186

South Asian (SAS) AF: 0.0763 AC: 368 AN: 4824

European-Finnish (FIN) AF: 0.0357 AC: 379 AN: 10604

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0422 AC: 2871 AN: 67998

Other (OTH) AF: 0.0941 AC: 199 AN: 2114

Alfa AF: 0.0739 Hom.: 134

Bravo AF: 0.120

Asia WGS AF: 0.0780 AC: 273 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	6.1
DANN	Benign	0.42
PhyloP100		0.81

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: rs11910746;

hg19: chr21-32396568;