chr3-183817188-G-A

Position:

• chr3-183817188-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.838

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]

ACMG classification

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	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	c.*168C>T		3_prime_UTR_variant	3/3	1	NM_024871.4	P1
MAP6D1	ENST00000431348.1	c.*168C>T		3_prime_UTR_variant	3/3	2

Frequencies

GnomAD3 genomes AF: 0.415 AC: 63026 AN: 151932 Hom.: 13366 Cov.: 33

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.: 6 AF XY: 0.449 AC XY: 113914 AN XY: 253748

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.: 33 AF XY: 0.408 AC XY: 30296 AN XY: 74314

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

Other links and lift over

dbSNP: rs2255015; hg19: chr3-183534976; COSMIC: COSV59374337; COSMIC: COSV59374337;