7-100958913-A-T

Variant names:

• chr7-100958913-A-T
• rs371082444
• NM_005960.2:c.7134A>T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_Strong BP7

The NM_005960.2(MUC3A):​c.7134A>T​(p.Ser2378Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. 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 0.0036 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MUC3A NM_005960.2 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -5.24

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 -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BP7: Synonymous conserved (PhyloP=-5.24 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MUC3A	NM_005960.2	c.7134A>T	p.Ser2378Ser	synonymous_variant	Exon 2 of 12	ENST00000379458.9	NP_005951.1
LOC105375431	XR_007060457.1	n.43+3360T>A		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MUC3A	ENST00000379458.9	c.7134A>T	p.Ser2378Ser	synonymous_variant	Exon 2 of 12	5	NM_005960.2	ENSP00000368771.5
MUC3A	ENST00000483366.5	c.7134A>T	p.Ser2378Ser	synonymous_variant	Exon 2 of 11	5		ENSP00000483541.1
MUC3A	ENST00000414964.5	n.948A>T		non_coding_transcript_exon_variant	Exon 1 of 10	5		ENSP00000393306.2

Frequencies

GnomAD3 genomes AF: 0.00 AC: 18 AN: 4940 Hom.: 0 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.00163

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00731

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00562

Gnomad SAS AF: 0.00485

Gnomad FIN AF: 0.00281

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00378

Gnomad OTH AF: 0.00

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0 AN: 1071324 Hom.: 0 Cov.: 111 AF XY: 0.00 AC XY: 0 AN XY: 513730

Gnomad4 AFR exome AF: 0.00

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 Data not reliable, filtered out with message: AS_VQSR AF: 0.00365 AC: 18 AN: 4936 Hom.: 0 Cov.: 0 AF XY: 0.00491 AC XY: 12 AN XY: 2442

Gnomad4 AFR AF: 0.00163

Gnomad4 AMR AF: 0.00731

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00568

Gnomad4 SAS AF: 0.00490

Gnomad4 FIN AF: 0.00281

Gnomad4 NFE AF: 0.00378

Gnomad4 OTH AF: 0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.5
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs371082444; hg19: chr7-100551042;