rs9501035

Variant names:

• chr6-30944637-G-A
• rs9501035
• NM_080870.4:c.82+3556G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
MUCL3	NM_080870.4	c.82+3556G>A		intron_variant	Intron 1 of 2	ENST00000462446.6	NP_543146.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MUCL3	ENST00000462446.6	c.82+3556G>A		intron_variant	Intron 1 of 2	5	NM_080870.4	ENSP00000417182.1
SFTA2	ENST00000634371.2	n.513+7725C>T		intron_variant	Intron 4 of 5	5

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

African (AFR) AF: 0.144 AC: 5992 AN: 41504

American (AMR) AF: 0.329 AC: 5039 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 695 AN: 3462

East Asian (EAS) AF: 0.560 AC: 2902 AN: 5178

South Asian (SAS) AF: 0.472 AC: 2269 AN: 4808

European-Finnish (FIN) AF: 0.239 AC: 2529 AN: 10568

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.162 AC: 11005 AN: 67980

Other (OTH) AF: 0.204 AC: 430 AN: 2106

Alfa AF: 0.179 Hom.: 4208

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
PhyloP100		1.3
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9501035; hg19: chr6-30912414;