rs1656377

Variant names:

• chr3-158567491-T-C
• rs1656377
• ENST00000475981.6:n.993+469A>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.993+469A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 151,988 control chromosomes in the GnomAD database, including 28,632 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 0.61 (28632 hom., cov: 32)
• Consequence: MLF1-DT ENST00000475981.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.706 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.993+469A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MLF1-DT	ENST00000475981.6	TSL:2	n.993+469A>G		intron	N/A
	MLF1-DT	ENST00000479233.1	TSL:2	n.288+469A>G		intron	N/A
	MLF1-DT	ENST00000662951.1		n.441+469A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92267 AN: 151870 Hom.: 28598 Cov.: 32

Gnomad AFR AF: 0.712

Gnomad AMI AF: 0.410

Gnomad AMR AF: 0.564

Gnomad ASJ AF: 0.532

Gnomad EAS AF: 0.341

Gnomad SAS AF: 0.666

Gnomad FIN AF: 0.562

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.584

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.608 AC: 92352 AN: 151988 Hom.: 28632 Cov.: 32 AF XY: 0.606 AC XY: 45020 AN XY: 74292

African (AFR) AF: 0.712 AC: 29538 AN: 41460

American (AMR) AF: 0.564 AC: 8606 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.532 AC: 1842 AN: 3460

East Asian (EAS) AF: 0.340 AC: 1757 AN: 5162

South Asian (SAS) AF: 0.665 AC: 3207 AN: 4820

European-Finnish (FIN) AF: 0.562 AC: 5940 AN: 10570

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

European-Non Finnish (NFE) AF: 0.584 AC: 39666 AN: 67936

Other (OTH) AF: 0.585 AC: 1234 AN: 2110

Alfa AF: 0.588 Hom.: 44764

Bravo AF: 0.608

Asia WGS AF: 0.565 AC: 1963 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.91
DANN	Benign	0.49
PhyloP100		-0.16

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: rs1656377;

hg19: chr3-158285280;