rs1630524

chr3-158552510-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_104147.1(MLF1-DT):n.1282+1352A>G variant causes a intron, non coding transcript 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 NR_104147.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.271

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MLF1-DT	NR_104147.1	n.1282+1352A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLF1-DT	ENST00000475981.6	n.1282+1352A>G		intron_variant, non_coding_transcript_variant		2
MLF1-DT	ENST00000662951.1	n.621+1352A>G		intron_variant, non_coding_transcript_variant
MLF1-DT	ENST00000667491.1	n.1158+1352A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.474

Gnomad4 AMR AF: 0.475

Gnomad4 ASJ AF: 0.429

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.542

Gnomad4 FIN AF: 0.469

Gnomad4 NFE AF: 0.477

Gnomad4 OTH AF: 0.448

Alfa AF: 0.473 Hom.: 33973

Bravo AF: 0.463

Asia WGS AF: 0.452 AC: 1567 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.1
Dann	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1630524; hg19: chr3-158270299;