rs2240803

chr6-30953180-G-Achr6-30953180-G-C

Variant summary

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

The NM_080870.4(MUCL3):c.*63G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.196 in 1,581,934 control chromosomes in the GnomAD database, including 37,061 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 0.18 (3248 hom., cov: 32)
  • Exomes 𝑓: 0.20 (33813 hom.)
• Consequence: MUCL3 NM_080870.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0150

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]

HCG21 (HGNC:31335): (HLA complex group 21)

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.44 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MUCL3	NM_080870.4	c.*63G>A		3_prime_UTR_variant	3/3	ENST00000462446.6
HCG21	NR_138040.1	n.87-649C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MUCL3	ENST00000462446.6	c.*63G>A		3_prime_UTR_variant	3/3	5	NM_080870.4	A2
HCG21	ENST00000419481.1	n.111C>T		non_coding_transcript_exon_variant	2/3	3
SFTA2	ENST00000634371.1	c.-301C>T		5_prime_UTR_variant	3/6	5
MUCL3	ENST00000636043.1	c.*63G>A		3_prime_UTR_variant	6/6	5		P4

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27910 AN: 152106 Hom.: 3234 Cov.: 32

Gnomad AFR AF: 0.0907

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.300

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.382

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.240

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.168

Gnomad OTH AF: 0.182

GnomAD4 exome AF: 0.197 AC: 281498 AN: 1429710 Hom.: 33813 Cov.: 32 AF XY: 0.204 AC XY: 144830 AN XY: 709620

Gnomad4 AFR exome AF: 0.0864

Gnomad4 AMR exome AF: 0.387

Gnomad4 ASJ exome AF: 0.211

Gnomad4 EAS exome AF: 0.422

Gnomad4 SAS exome AF: 0.450

Gnomad4 FIN exome AF: 0.242

Gnomad4 NFE exome AF: 0.163

Gnomad4 OTH exome AF: 0.216

GnomAD4 genome AF: 0.184 AC: 27945 AN: 152224 Hom.: 3248 Cov.: 32 AF XY: 0.196 AC XY: 14551 AN XY: 74414

Gnomad4 AFR AF: 0.0906

Gnomad4 AMR AF: 0.300

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.382

Gnomad4 SAS AF: 0.456

Gnomad4 FIN AF: 0.240

Gnomad4 NFE AF: 0.168

Gnomad4 OTH AF: 0.190

Alfa AF: 0.178 Hom.: 3868

Bravo AF: 0.178

Asia WGS AF: 0.461 AC: 1601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.3
Dann	Benign	0.78

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: rs2240803; hg19: chr6-30920957; COSMIC: COSV58517563;