chr1-36171247-C-T

Variant names:

• chr1-36171247-C-T
• rs1384509886
• NM_001388490.1:c.323C>T

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001388490.1(MAP7D1):​c.323C>T​(p.Pro108Leu) variant causes a missense 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. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 31)
• Consequence: MAP7D1 NM_001388490.1 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 1.07
• Publications: 0 publications found

Genes affected

MAP7D1 (HGNC:25514): (MAP7 domain containing 1) Predicted to be involved in microtubule cytoskeleton organization. Located in cytosol and microtubule cytoskeleton. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.17381924).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001388490.1. 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
	MAP7D1	NM_001388490.1	MANE Select	c.323C>T	p.Pro108Leu	missense	Exon 2 of 17	NP_001375419.1	D3DPS3
	MAP7D1	NM_018067.5		c.323C>T	p.Pro108Leu	missense	Exon 2 of 17	NP_060537.3
	MAP7D1	NM_001286366.2		c.323C>T	p.Pro108Leu	missense	Exon 2 of 18	NP_001273295.1	Q3KQU3-4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP7D1	ENST00000474796.2	TSL:2 MANE Select	c.323C>T	p.Pro108Leu	missense	Exon 2 of 17	ENSP00000507044.1	D3DPS3
	MAP7D1	ENST00000373151.6	TSL:1	c.323C>T	p.Pro108Leu	missense	Exon 2 of 17	ENSP00000362244.2	Q3KQU3-1
	MAP7D1	ENST00000316156.8	TSL:1	c.323C>T	p.Pro108Leu	missense	Exon 2 of 16	ENSP00000320228.4	Q3KQU3-2

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 31

Asia WGS AF: 0.000289 AC: 1 AN: 3478

ClinVar

ClinVar submissions

Significance: Uncertain significance

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	1	-	not specified (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.080
BayesDel_addAF	Benign	-0.11	T
BayesDel_noAF	Benign	-0.40
CADD	Uncertain	25
DANN	Uncertain	1.0
DEOGEN2	Benign	0.014	T
Eigen	Uncertain	0.20
Eigen_PC	Benign	0.18
FATHMM_MKL	Benign	0.26	N
LIST_S2	Uncertain	0.93	D
M_CAP	Benign	0.017	T
MetaRNN	Benign	0.17	T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	1.8	L
PhyloP100		1.1
PrimateAI	Benign	0.42	T
PROVEAN	Uncertain	-2.8	D
REVEL	Benign	0.071
Sift	Uncertain	0.0020	D
Sift4G	Uncertain	0.017	D
Polyphen		0.94	P
Vest4		0.36
MutPred		0.39		Gain of MoRF binding (P = 0.023)
MVP		0.12
MPC		0.58
ClinPred		0.96	D
GERP RS		4.7
Varity_R		0.19
gMVP		0.27
Mutation Taster		=96/4	polymorphism

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: rs1384509886; hg19: chr1-36636848;