NM_021201.5:c.*317T>A

Variant names:

• chr11-60394178-T-A
• rs1892
• NM_021201.5:c.*317T>A

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_021201.5(MS4A7):​c.*317T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MS4A7 NM_021201.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17
• Publications: 11 publications found

Genes affected

MS4A7 (HGNC:13378): (membrane spanning 4-domains A7) This gene encodes a member of the membrane-spanning 4A gene family, members of which are characterized by common structural features and similar intron/exon splice boundaries and display unique expression patterns in hematopoietic cells and nonlymphoid tissues. This family member is associated with mature cellular function in the monocytic lineage, and it may be a component of a receptor complex involved in signal transduction. This gene is localized to 11q12, in a cluster of other family members. At least four alternatively spliced transcript variants encoding two distinct isoforms have been observed. [provided by RefSeq, Jul 2008]

MS4A14 (HGNC:30706): (membrane spanning 4-domains A14) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

MS4A6E (HGNC:14285): (membrane spanning 4-domains A6E) This gene encodes a member of the membrane-spanning 4A gene family. Members of this nascent protein family are characterized by common structural features and similar intron/exon splice boundaries and display unique expression patterns among hematopoietic cells and nonlymphoid tissues. The gene encoding this protein is localized to 11q12.3, among a cluster of family members. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_021201.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MS4A7	NM_021201.5	MANE Select	c.*317T>A		3_prime_UTR	Exon 7 of 7	NP_067024.1
	MS4A7	NM_206939.2		c.*317T>A		3_prime_UTR	Exon 7 of 7	NP_996822.1
	MS4A7	NM_206938.2		c.*317T>A		3_prime_UTR	Exon 6 of 6	NP_996821.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MS4A7	ENST00000300184.8	TSL:1 MANE Select	c.*317T>A		3_prime_UTR	Exon 7 of 7	ENSP00000300184.3
	MS4A7	ENST00000358246.5	TSL:3	c.*317T>A		3_prime_UTR	Exon 6 of 6	ENSP00000350983.1
	MS4A7	ENST00000534016.5	TSL:2	c.*317T>A		3_prime_UTR	Exon 6 of 6	ENSP00000434637.1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 54106 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 27520

African (AFR) AF: 0.00 AC: 0 AN: 1932

American (AMR) AF: 0.00 AC: 0 AN: 1814

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2378

East Asian (EAS) AF: 0.00 AC: 0 AN: 3626

South Asian (SAS) AF: 0.00 AC: 0 AN: 1212

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 2506

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 292

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 36542

Other (OTH) AF: 0.00 AC: 0 AN: 3804

GnomAD4 genome Cov.: 31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.62
DANN	Benign	0.63
PhyloP100		-1.2

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: rs1892; hg19: chr11-60161651;