chr3-21224638-A-T

Variant names:

• chr3-21224638-A-T
• rs727611
• ENST00000634947.1:n.370+50T>A

Variant summary

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

The ENST00000726596.1(ENSG00000294894):​n.46+13587A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.841 in 152,204 control chromosomes in the GnomAD database, including 53,952 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 0.84 (53952 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ENSG00000294894 ENST00000726596.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25
• Publications: 2 publications found

Genes affected

ENSG00000282987 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000726596.1. 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
	ENSG00000282987	ENST00000634947.1	TSL:5	n.370+50T>A		intron	N/A
	ENSG00000294894	ENST00000726596.1		n.46+13587A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.841 AC: 127854 AN: 152084 Hom.: 53909 Cov.: 32

Gnomad AFR AF: 0.880

Gnomad AMI AF: 0.798

Gnomad AMR AF: 0.861

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.915

Gnomad FIN AF: 0.811

Gnomad MID AF: 0.848

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.828

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.841 AC: 127955 AN: 152202 Hom.: 53952 Cov.: 32 AF XY: 0.844 AC XY: 62803 AN XY: 74420

African (AFR) AF: 0.880 AC: 36554 AN: 41532

American (AMR) AF: 0.861 AC: 13168 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.786 AC: 2725 AN: 3468

East Asian (EAS) AF: 0.999 AC: 5165 AN: 5170

South Asian (SAS) AF: 0.915 AC: 4417 AN: 4826

European-Finnish (FIN) AF: 0.811 AC: 8597 AN: 10594

Middle Eastern (MID) AF: 0.837 AC: 246 AN: 294

European-Non Finnish (NFE) AF: 0.803 AC: 54603 AN: 67996

Other (OTH) AF: 0.830 AC: 1752 AN: 2112

Alfa AF: 0.825 Hom.: 6064

Bravo AF: 0.846

Asia WGS AF: 0.946 AC: 3288 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.8
DANN	Benign	0.69
PhyloP100		1.3

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: rs727611;

hg19: chr3-21266130;