chr1-36171032-A-C

Position:

• chr1-36171032-A-C

Variant summary

Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_Strong BP6_Moderate BP7

The NM_001388490.1(MAP7D1):​c.108A>C​(p.Pro36Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.0083 (0 hom., cov: 0)
  • Exomes 𝑓: 0.0058 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MAP7D1 NM_001388490.1 synonymous
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.769

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]

MAP7D1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -7 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.57).
• BP6: Variant 1-36171032-A-C is Benign according to our data. Variant chr1-36171032-A-C is described in ClinVar as [Likely_benign]. Clinvar id is 2638668.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=-0.769 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MAP7D1	NM_001388490.1	c.108A>C	p.Pro36Pro	synonymous_variant	2/17	ENST00000474796.2	NP_001375419.1
MAP7D1	NM_018067.5	c.108A>C	p.Pro36Pro	synonymous_variant	2/17		NP_060537.3
MAP7D1	NM_001286366.2	c.108A>C	p.Pro36Pro	synonymous_variant	2/18		NP_001273295.1
MAP7D1	NM_001286365.2	c.108A>C	p.Pro36Pro	synonymous_variant	2/16		NP_001273294.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MAP7D1	ENST00000474796.2	c.108A>C	p.Pro36Pro	synonymous_variant	2/17	2	NM_001388490.1	ENSP00000507044.1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 353 AN: 42634 Hom.: 0 Cov.: 0 FAILED QC

Gnomad AFR AF: 0.00822

Gnomad AMI AF: 0.00758

Gnomad AMR AF: 0.00953

Gnomad ASJ AF: 0.00847

Gnomad EAS AF: 0.00422

Gnomad SAS AF: 0.00435

Gnomad FIN AF: 0.00431

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00893

Gnomad OTH AF: 0.0157

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00576 AC: 5357 AN: 929564 Hom.: 0 Cov.: 27 AF XY: 0.00648 AC XY: 2946 AN XY: 454932

Gnomad4 AFR exome AF: 0.00254

Gnomad4 AMR exome AF: 0.0110

Gnomad4 ASJ exome AF: 0.0102

Gnomad4 EAS exome AF: 0.00831

Gnomad4 SAS exome AF: 0.0253

Gnomad4 FIN exome AF: 0.00959

Gnomad4 NFE exome AF: 0.00412

Gnomad4 OTH exome AF: 0.00806

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00827 AC: 353 AN: 42708 Hom.: 0 Cov.: 0 AF XY: 0.00783 AC XY: 164 AN XY: 20958

Gnomad4 AFR AF: 0.00818

Gnomad4 AMR AF: 0.00953

Gnomad4 ASJ AF: 0.00847

Gnomad4 EAS AF: 0.00422

Gnomad4 SAS AF: 0.00434

Gnomad4 FIN AF: 0.00431

Gnomad4 NFE AF: 0.00893

Gnomad4 OTH AF: 0.0154

Alfa AF: 0.0149 Hom.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

CeGaT Center for Human Genetics Tuebingen

Mar 01, 2023

MAP7D1: BP4, BP7 -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.57
CADD	Benign	7.5
DANN	Benign	0.70

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.090		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs530295377; hg19: chr1-36636633; COSMIC: COSV60215394; COSMIC: COSV60215394;