rs3132581

chr6-30945681-G-A

Variant summary

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

The NM_080870.4(MUCL3):c.83-2866G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.091 in 151,872 control chromosomes in the GnomAD database, including 802 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 0.091 (802 hom., cov: 31)
• Consequence: MUCL3 NM_080870.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.886

Genes affected

MUCL3 (HGNC:21666): (mucin like 3) Predicted to be located in cytoplasm and plasma membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

SFTA2 (HGNC:18386): (surfactant associated 2) Predicted to be located in Golgi apparatus; extracellular region; and transport vesicle. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.133 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MUCL3	NM_080870.4	c.83-2866G>A		intron_variant		ENST00000462446.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MUCL3	ENST00000462446.6	c.83-2866G>A		intron_variant		5	NM_080870.4	A2
SFTA2	ENST00000634371.1	c.-9+6681C>T		intron_variant		5
MUCL3	ENST00000636043.1	c.284-2866G>A		intron_variant		5		P4

Frequencies

GnomAD3 genomes AF: 0.0910 AC: 13810 AN: 151756 Hom.: 802 Cov.: 31

Gnomad AFR AF: 0.0622

Gnomad AMI AF: 0.144

Gnomad AMR AF: 0.0366

Gnomad ASJ AF: 0.0652

Gnomad EAS AF: 0.0201

Gnomad SAS AF: 0.0129

Gnomad FIN AF: 0.0760

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.135

Gnomad OTH AF: 0.0705

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

GnomAD4 genome AF: 0.0910 AC: 13824 AN: 151872 Hom.: 802 Cov.: 31 AF XY: 0.0842 AC XY: 6252 AN XY: 74212

Gnomad4 AFR AF: 0.0625

Gnomad4 AMR AF: 0.0364

Gnomad4 ASJ AF: 0.0652

Gnomad4 EAS AF: 0.0202

Gnomad4 SAS AF: 0.0127

Gnomad4 FIN AF: 0.0760

Gnomad4 NFE AF: 0.135

Gnomad4 OTH AF: 0.0693

Alfa AF: 0.125 Hom.: 1374

Bravo AF: 0.0891

Asia WGS AF: 0.0180 AC: 63 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.44
Dann	Benign	0.25

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3132581; hg19: chr6-30913458;