3-21200164-T-C

Variant names:

• chr3-21200164-T-C
• rs1898300
• ENST00000634947.1:n.370+24524A>G

Variant summary

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

The ENST00000634947.1(ENSG00000282987):​n.370+24524A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 151,222 control chromosomes in the GnomAD database, including 22,363 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 0.52 (22363 hom., cov: 31)
• Consequence: ENSG00000282987 ENST00000634947.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01
• 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=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000634947.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000282987	ENST00000634947.1	TSL:5	n.370+24524A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.518 AC: 78324 AN: 151102 Hom.: 22324 Cov.: 31

Gnomad AFR AF: 0.706

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.368

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.685

Gnomad FIN AF: 0.447

Gnomad MID AF: 0.510

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.497

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

GnomAD4 genome AF: 0.519 AC: 78426 AN: 151222 Hom.: 22363 Cov.: 31 AF XY: 0.529 AC XY: 39117 AN XY: 73924

African (AFR) AF: 0.706 AC: 29202 AN: 41352

American (AMR) AF: 0.586 AC: 8900 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.368 AC: 1277 AN: 3466

East Asian (EAS) AF: 0.850 AC: 4378 AN: 5152

South Asian (SAS) AF: 0.685 AC: 3297 AN: 4812

European-Finnish (FIN) AF: 0.447 AC: 4629 AN: 10346

Middle Eastern (MID) AF: 0.500 AC: 133 AN: 266

European-Non Finnish (NFE) AF: 0.375 AC: 25365 AN: 67628

Other (OTH) AF: 0.498 AC: 1043 AN: 2094

Alfa AF: 0.466 Hom.: 2993

Bravo AF: 0.537

Asia WGS AF: 0.761 AC: 2601 AN: 3420

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.97
DANN	Benign	0.21
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs1898300; hg19: chr3-21241656;