3-120458253-A-T

Variant names:

• chr3-120458253-A-T
• rs1270209
• ENST00000659560.1:n.179+9101A>T

Variant summary

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

The ENST00000659560.1(ENSG00000286735):​n.179+9101A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.408 in 152,114 control chromosomes in the GnomAD database, including 15,304 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 0.41 (15304 hom., cov: 32)
• Consequence: ENSG00000286735 ENST00000659560.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.47
• Publications: 5 publications found

Genes affected

ENSG00000286735 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.674 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286735	ENST00000659560.1	n.179+9101A>T		intron_variant	Intron 1 of 2
ENSG00000286735	ENST00000732215.1	n.95+9092A>T		intron_variant	Intron 1 of 3
ENSG00000286735	ENST00000732216.1	n.172+9092A>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.408 AC: 62048 AN: 151996 Hom.: 15264 Cov.: 32

Gnomad AFR AF: 0.680

Gnomad AMI AF: 0.178

Gnomad AMR AF: 0.495

Gnomad ASJ AF: 0.396

Gnomad EAS AF: 0.209

Gnomad SAS AF: 0.259

Gnomad FIN AF: 0.205

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.419

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

GnomAD4 genome AF: 0.408 AC: 62135 AN: 152114 Hom.: 15304 Cov.: 32 AF XY: 0.405 AC XY: 30094 AN XY: 74362

African (AFR) AF: 0.680 AC: 28222 AN: 41476

American (AMR) AF: 0.495 AC: 7565 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.396 AC: 1375 AN: 3470

East Asian (EAS) AF: 0.209 AC: 1082 AN: 5186

South Asian (SAS) AF: 0.257 AC: 1239 AN: 4814

European-Finnish (FIN) AF: 0.205 AC: 2171 AN: 10598

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.284 AC: 19331 AN: 67980

Other (OTH) AF: 0.417 AC: 880 AN: 2110

Alfa AF: 0.350 Hom.: 1402

Bravo AF: 0.443

Asia WGS AF: 0.259 AC: 904 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.095
DANN	Benign	0.31
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs1270209; hg19: chr3-120177100;