rs1714524

Variant names:

• chr3-158555307-C-T
• rs1714524
• ENST00000475981.6:n.1103-1266G>A

Variant summary

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

The ENST00000475981.6(MLF1-DT):​n.1103-1266G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.595 in 152,086 control chromosomes in the GnomAD database, including 27,675 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 0.60 (27675 hom., cov: 32)
• Consequence: MLF1-DT ENST00000475981.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.671
• Publications: 13 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.722 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MLF1-DT	NR_104147.1	n.1103-1266G>A		intron_variant	Intron 3 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MLF1-DT	ENST00000475981.6	n.1103-1266G>A		intron_variant	Intron 3 of 4	2
MLF1-DT	ENST00000479233.1	n.289-1266G>A		intron_variant	Intron 3 of 3	2
MLF1-DT	ENST00000662951.1	n.442-1266G>A		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes AF: 0.595 AC: 90430 AN: 151968 Hom.: 27633 Cov.: 32

Gnomad AFR AF: 0.729

Gnomad AMI AF: 0.409

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.361

Gnomad SAS AF: 0.644

Gnomad FIN AF: 0.539

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.553

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.595 AC: 90527 AN: 152086 Hom.: 27675 Cov.: 32 AF XY: 0.595 AC XY: 44210 AN XY: 74346

African (AFR) AF: 0.729 AC: 30258 AN: 41506

American (AMR) AF: 0.563 AC: 8602 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1696 AN: 3464

East Asian (EAS) AF: 0.361 AC: 1869 AN: 5176

South Asian (SAS) AF: 0.643 AC: 3091 AN: 4806

European-Finnish (FIN) AF: 0.539 AC: 5681 AN: 10548

Middle Eastern (MID) AF: 0.639 AC: 188 AN: 294

European-Non Finnish (NFE) AF: 0.553 AC: 37581 AN: 67988

Other (OTH) AF: 0.563 AC: 1189 AN: 2112

Alfa AF: 0.566 Hom.: 76687

Bravo AF: 0.598

Asia WGS AF: 0.570 AC: 1981 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	1.2
DANN	Benign	0.61
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs1714524; hg19: chr3-158273096;