rs3757340

chr6-30954105-T-Cchr6-30954105-T-G

Variant summary

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

The NM_080870.4(MUCL3):c.*988T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 152,122 control chromosomes in the GnomAD database, including 10,700 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 0.36 (10697 hom., cov: 31)
  • Exomes 𝑓: 0.29 (3 hom.)
• Consequence: MUCL3 NM_080870.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497

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=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.509 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MUCL3	NM_080870.4	c.*988T>C		3_prime_UTR_variant	3/3	ENST00000462446.6
HCG21	NR_138040.1	n.86+672A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MUCL3	ENST00000462446.6	c.*988T>C		3_prime_UTR_variant	3/3	5	NM_080870.4	A2
HCG21	ENST00000419481.1	n.86+672A>G		intron_variant, non_coding_transcript_variant		3
MUCL3	ENST00000636043.1	c.*988T>C		3_prime_UTR_variant	6/6	5		P4
SFTA2	ENST00000634371.1	c.-326+672A>G		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55291 AN: 151946 Hom.: 10673 Cov.: 31

Gnomad AFR AF: 0.446

Gnomad AMI AF: 0.396

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.282

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.526

Gnomad FIN AF: 0.332

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.282

Gnomad OTH AF: 0.396

GnomAD4 exome AF: 0.293 AC: 17 AN: 58 Hom.: 3 Cov.: 0 AF XY: 0.321 AC XY: 9 AN XY: 28

Gnomad4 FIN exome AF: 0.265

Gnomad4 NFE exome AF: 0.318

GnomAD4 genome AF: 0.364 AC: 55354 AN: 152064 Hom.: 10697 Cov.: 31 AF XY: 0.372 AC XY: 27650 AN XY: 74318

Gnomad4 AFR AF: 0.446

Gnomad4 AMR AF: 0.466

Gnomad4 ASJ AF: 0.282

Gnomad4 EAS AF: 0.430

Gnomad4 SAS AF: 0.526

Gnomad4 FIN AF: 0.332

Gnomad4 NFE AF: 0.282

Gnomad4 OTH AF: 0.402

Alfa AF: 0.299 Hom.: 13270

Bravo AF: 0.374

Asia WGS AF: 0.545 AC: 1894 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.98
Dann	Benign	0.68

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: rs3757340; hg19: chr6-30921882;