rs1714524

Positions:

• chr3-158555307-C-T

Variant summary

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

The NR_104147.1(MLF1-DT):​n.1103-1266G>A 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 0.595 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 NR_104147.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.671

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=-0.95).
• 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/exons	MANE	UniProt
MLF1-DT	NR_104147.1	n.1103-1266G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLF1-DT	ENST00000475981.6	n.1103-1266G>A		intron_variant, non_coding_transcript_variant		2
MLF1-DT	ENST00000479233.1	n.289-1266G>A		intron_variant, non_coding_transcript_variant		2
MLF1-DT	ENST00000662951.1	n.442-1266G>A		intron_variant, non_coding_transcript_variant
MLF1-DT	ENST00000667491.1	n.979-1266G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.729

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.490

Gnomad4 EAS AF: 0.361

Gnomad4 SAS AF: 0.643

Gnomad4 FIN AF: 0.539

Gnomad4 NFE AF: 0.553

Gnomad4 OTH AF: 0.563

Alfa AF: 0.554 Hom.: 47548

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1714524; hg19: chr3-158273096;