rs1630524

Variant names:

• chr3-158552510-T-C
• rs1630524
• ENST00000475981.6:n.1282+1352A>G

Variant summary

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

The ENST00000475981.6(MLF1-DT):​n.1282+1352A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.468 in 152,066 control chromosomes in the GnomAD database, including 16,769 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 0.47 (16769 hom., cov: 32)
• Consequence: MLF1-DT ENST00000475981.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271
• Publications: 10 publications found

Genes affected

MLF1-DT (HGNC:55620): (MLF1 divergent transcript)

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 (SAS) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000475981.6. 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
	MLF1-DT	NR_104147.1		n.1282+1352A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MLF1-DT	ENST00000475981.6	TSL:2	n.1282+1352A>G		intron	N/A
	MLF1-DT	ENST00000662951.1		n.621+1352A>G		intron	N/A
	MLF1-DT	ENST00000667491.1		n.1158+1352A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71100 AN: 151948 Hom.: 16759 Cov.: 32

Gnomad AFR AF: 0.474

Gnomad AMI AF: 0.404

Gnomad AMR AF: 0.475

Gnomad ASJ AF: 0.429

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.542

Gnomad FIN AF: 0.469

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.477

Gnomad OTH AF: 0.445

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

GnomAD4 genome AF: 0.468 AC: 71160 AN: 152066 Hom.: 16769 Cov.: 32 AF XY: 0.469 AC XY: 34847 AN XY: 74334

African (AFR) AF: 0.474 AC: 19675 AN: 41468

American (AMR) AF: 0.475 AC: 7255 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.429 AC: 1488 AN: 3468

East Asian (EAS) AF: 0.243 AC: 1255 AN: 5172

South Asian (SAS) AF: 0.542 AC: 2614 AN: 4824

European-Finnish (FIN) AF: 0.469 AC: 4961 AN: 10570

Middle Eastern (MID) AF: 0.541 AC: 158 AN: 292

European-Non Finnish (NFE) AF: 0.477 AC: 32438 AN: 67968

Other (OTH) AF: 0.448 AC: 948 AN: 2114

Alfa AF: 0.474 Hom.: 71009

Bravo AF: 0.463

Asia WGS AF: 0.452 AC: 1567 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	3.1
DANN	Benign	0.86
PhyloP100		-0.27

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: rs1630524;

hg19: chr3-158270299;