Variant rs2255015 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024871.4(MAP6D1):c.*168C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 633,324 control chromosomes in the GnomAD database, including 62,045 homozygotes. 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 0.41 ( 13365 hom., cov: 33)

Exomes 𝑓: 0.45 ( 48680 hom. )

Consequence

MAP6D1
NM_024871.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.838

Variant links:

Genes affected

MAP6D1 (HGNC:25753): (MAP6 domain containing 1) This gene encodes a protein highly similar to the mouse MAP6 domain containing 1 protein, which is related to the STOP proteins. Based on the study of the mouse protein, the encoded protein may function as a calmodulin-regulated neuronal protein that binds and stabilizes microtubules but also associates with the Golgi membranes through N-terminal palmitoylation. [provided by RefSeq, Oct 2008]

MAP6D1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.455 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAP6D1	NM_024871.4 linkuse as main transcript	c.*168C>T		3_prime_UTR_variant	3/3	ENST00000318631.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP6D1	ENST00000318631.8 linkuse as main transcript	c.*168C>T		3_prime_UTR_variant	3/3	1	NM_024871.4	P1
MAP6D1	ENST00000431348.1 linkuse as main transcript	c.*168C>T		3_prime_UTR_variant	3/3	2

Frequencies

GnomAD3 genomes

AF:

0.415

AC:

63026

AN:

151932

Hom.:

13366

Cov.:

show subpopulations

Gnomad AFR

AF:

0.349

Gnomad AMI

AF:

0.364

Gnomad AMR

AF:

0.429

Gnomad ASJ

AF:

0.493

Gnomad EAS

AF:

0.397

Gnomad SAS

AF:

0.453

Gnomad FIN

AF:

0.325

Gnomad MID

AF:

0.544

Gnomad NFE

AF:

0.459

Gnomad OTH

AF:

0.469

GnomAD4 exome

AF:

0.447

AC:

215124

AN:

481274

Hom.:

48680

Cov.:

AF XY:

0.449

AC XY:

113914

AN XY:

253748

show subpopulations

Gnomad4 AFR exome

AF:

0.346

Gnomad4 AMR exome

AF:

0.418

Gnomad4 ASJ exome

AF:

0.497

Gnomad4 EAS exome

AF:

0.435

Gnomad4 SAS exome

AF:

0.446

Gnomad4 FIN exome

AF:

0.356

Gnomad4 NFE exome

AF:

0.462

Gnomad4 OTH exome

AF:

0.446

GnomAD4 genome

AF:

0.415

AC:

63041

AN:

152050

Hom.:

13365

Cov.:

AF XY:

0.408

AC XY:

30296

AN XY:

74314

show subpopulations

Gnomad4 AFR

AF:

0.349

Gnomad4 AMR

AF:

0.429

Gnomad4 ASJ

AF:

0.493

Gnomad4 EAS

AF:

0.398

Gnomad4 SAS

AF:

0.451

Gnomad4 FIN

AF:

0.325

Gnomad4 NFE

AF:

0.459

Gnomad4 OTH

AF:

0.464

Alfa

AF:

0.461

Hom.:

15981

Bravo

AF:

0.420

Asia WGS

AF:

0.442

AC:

1539

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.63

DANN

Benign

0.40

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over