rs9501035

Positions:

• chr6-30944637-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.82+3556G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.205 in 152,106 control chromosomes in the GnomAD database, including 4,062 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 0.20 (4062 hom., cov: 33)
• Consequence: MUCL3 NM_080870.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.25

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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.543 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MUCL3	NM_080870.4	c.82+3556G>A		intron_variant		ENST00000462446.6	NP_543146.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MUCL3	ENST00000462446.6	c.82+3556G>A		intron_variant		5	NM_080870.4	ENSP00000417182.1
MUCL3	ENST00000636043.1	c.283+3556G>A		intron_variant		5		ENSP00000490368.1
SFTA2	ENST00000634371.1	c.-9+7725C>T		intron_variant		5		ENSP00000489572.1

Frequencies

GnomAD3 genomes AF: 0.205 AC: 31141 AN: 151988 Hom.: 4050 Cov.: 33

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.560

Gnomad SAS AF: 0.472

Gnomad FIN AF: 0.239

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.205 AC: 31178 AN: 152106 Hom.: 4062 Cov.: 33 AF XY: 0.217 AC XY: 16102 AN XY: 74348

Gnomad4 AFR AF: 0.144

Gnomad4 AMR AF: 0.329

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.560

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.239

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.204

Alfa AF: 0.164 Hom.: 1288

Bravo AF: 0.204

Asia WGS AF: 0.505 AC: 1753 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	9.9
DANN	Benign	0.85

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: rs9501035; hg19: chr6-30912414;