rs2255015

Variant names:

• chr3-183817188-G-A
• rs2255015
• NM_024871.4:c.*168C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-183817188-G-A
• chr3-183817188-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 16 publications found

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]

ENSG00000283765 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_024871.4. 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
	MAP6D1	NM_024871.4	MANE Select	c.*168C>T		3_prime_UTR	Exon 3 of 3	NP_079147.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAP6D1	ENST00000318631.8	TSL:1 MANE Select	c.*168C>T		3_prime_UTR	Exon 3 of 3	ENSP00000314560.4
	ENSG00000283765	ENST00000639401.1	TSL:5	c.*168C>T		3_prime_UTR	Exon 11 of 11	ENSP00000491227.1
	MAP6D1	ENST00000431348.1	TSL:2	c.*168C>T		3_prime_UTR	Exon 3 of 3	ENSP00000388945.1

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

African (AFR) AF: 0.346 AC: 4572 AN: 13214

American (AMR) AF: 0.418 AC: 9307 AN: 22286

Ashkenazi Jewish (ASJ) AF: 0.497 AC: 7179 AN: 14448

East Asian (EAS) AF: 0.435 AC: 12865 AN: 29548

South Asian (SAS) AF: 0.446 AC: 21782 AN: 48888

European-Finnish (FIN) AF: 0.356 AC: 10990 AN: 30876

Middle Eastern (MID) AF: 0.535 AC: 1094 AN: 2044

European-Non Finnish (NFE) AF: 0.462 AC: 135457 AN: 293336

Other (OTH) AF: 0.446 AC: 11878 AN: 26634

GnomAD4 genome AF: 0.415 AC: 63041 AN: 152050 Hom.: 13365 Cov.: 33 AF XY: 0.408 AC XY: 30296 AN XY: 74314

African (AFR) AF: 0.349 AC: 14465 AN: 41478

American (AMR) AF: 0.429 AC: 6561 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1710 AN: 3472

East Asian (EAS) AF: 0.398 AC: 2051 AN: 5154

South Asian (SAS) AF: 0.451 AC: 2174 AN: 4822

European-Finnish (FIN) AF: 0.325 AC: 3427 AN: 10560

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.459 AC: 31179 AN: 67958

Other (OTH) AF: 0.464 AC: 981 AN: 2112

Alfa AF: 0.454 Hom.: 20434

Bravo AF: 0.420

Asia WGS AF: 0.442 AC: 1539 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	0.63
DANN	Benign	0.40
PhyloP100		-0.84
Mutation Taster		=100/0	polymorphism (auto)

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