rs2240803

Variant names:

• chr6-30953180-G-A
• rs2240803
• NM_080870.4:c.*63G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-30953180-G-A
• chr6-30953180-G-C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 21 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]

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_080870.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MUCL3	NM_080870.4	MANE Select	c.*63G>A		3_prime_UTR	Exon 3 of 3	NP_543146.2	E9PEI6
	HCG21	NR_138040.1		n.87-649C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MUCL3	ENST00000462446.6	TSL:5 MANE Select	c.*63G>A		3_prime_UTR	Exon 3 of 3	ENSP00000417182.1	E9PEI6
	HCG21	ENST00000419481.1	TSL:3	n.111C>T		non_coding_transcript_exon	Exon 2 of 3
	SFTA2	ENST00000634371.2	TSL:5	n.221C>T		non_coding_transcript_exon	Exon 3 of 6

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

African (AFR) AF: 0.0864 AC: 2813 AN: 32542

American (AMR) AF: 0.387 AC: 15906 AN: 41102

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 5101 AN: 24134

East Asian (EAS) AF: 0.422 AC: 16650 AN: 39444

South Asian (SAS) AF: 0.450 AC: 36805 AN: 81734

European-Finnish (FIN) AF: 0.242 AC: 11607 AN: 47972

Middle Eastern (MID) AF: 0.211 AC: 965 AN: 4578

European-Non Finnish (NFE) AF: 0.163 AC: 178880 AN: 1099136

Other (OTH) AF: 0.216 AC: 12771 AN: 59068

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

African (AFR) AF: 0.0906 AC: 3762 AN: 41534

American (AMR) AF: 0.300 AC: 4596 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 698 AN: 3472

East Asian (EAS) AF: 0.382 AC: 1978 AN: 5180

South Asian (SAS) AF: 0.456 AC: 2200 AN: 4822

European-Finnish (FIN) AF: 0.240 AC: 2546 AN: 10598

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.168 AC: 11449 AN: 68002

Other (OTH) AF: 0.190 AC: 401 AN: 2114

Alfa AF: 0.177 Hom.: 7206

Bravo AF: 0.178

Asia WGS AF: 0.461 AC: 1601 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.3
DANN	Benign	0.78
PhyloP100		0.015
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: rs2240803; hg19: chr6-30920957; COSMIC: COSV58517563;