7-100958760-G-T

Variant names:

• chr7-100958760-G-T
• rs111579886
• NM_005960.2:c.6981G>T

Variant summary

Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2 BP4_Strong BP7

The NM_005960.2(MUC3A):​c.6981G>T​(p.Ser2327Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000375 in 800,274 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.0013 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0000025 (0 hom.)
• Consequence: MUC3A NM_005960.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.09

Genes affected

MUC3A (HGNC:7513): (mucin 3A, cell surface associated) The mucin genes encode epithelial glycoproteins, some of which are secreted and some membrane bound. Each of the genes contains at least one large domain of tandemly repeated sequence that encodes the peptide sequence rich in serine and/or threonine residues, which carries most of the O-linked glycosylation (Gendler and Spicer, 1995 [PubMed 7778880]).[supplied by OMIM, Aug 2008]

LOC105375431 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BP7: Synonymous conserved (PhyloP=-5.09 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MUC3A	NM_005960.2	c.6981G>T	p.Ser2327Ser	synonymous_variant	Exon 2 of 12	ENST00000379458.9	NP_005951.1
LOC105375431	XR_007060457.1	n.43+3513C>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MUC3A	ENST00000379458.9	c.6981G>T	p.Ser2327Ser	synonymous_variant	Exon 2 of 12	5	NM_005960.2	ENSP00000368771.5
MUC3A	ENST00000483366.5	c.6981G>T	p.Ser2327Ser	synonymous_variant	Exon 2 of 11	5		ENSP00000483541.1
MUC3A	ENST00000414964.5	n.795G>T		non_coding_transcript_exon_variant	Exon 1 of 10	5		ENSP00000393306.2

Frequencies

GnomAD3 genomes AF: 0.00126 AC: 1 AN: 794 Hom.: 0 Cov.: 0

Gnomad AFR AF: 0.00676

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

GnomAD3 exomes AF: 0.0000121 AC: 2 AN: 164754 Hom.: 0 AF XY: 0.0000106 AC XY: 1 AN XY: 94286

Gnomad AFR exome AF: 0.000243

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.00000250 AC: 2 AN: 799480 Hom.: 0 Cov.: 102 AF XY: 0.00000260 AC XY: 1 AN XY: 384412

Gnomad4 AFR exome AF: 0.000124

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.00126 AC: 1 AN: 794 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 404

Gnomad4 AFR AF: 0.00676

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.00

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.2
DANN	Benign	0.46

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs111579886; hg19: chr7-100550889;