11-75606128-G-A

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_033063.2(MAP6):c.1120-124C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 1,138,626 control chromosomes in the GnomAD database, including 8,300 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.086 (763 hom., cov: 32)
  • Exomes 𝑓: 0.12 (7537 hom.)
• Consequence: MAP6 NM_033063.2 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.971

Genes affected

MAP6 (HGNC:6868): (microtubule associated protein 6) This gene encodes a microtubule-associated protein. The encoded protein is a calmodulin-binding and calmodulin-regulated protein that is involved in microtubule stabilization. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BP6: Variant 11-75606128-G-A is Benign according to our data. Variant chr11-75606128-G-A is described in ClinVar as [Benign]. Clinvar id is 1270127.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.12 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MAP6	NM_033063.2	c.1120-124C>T		intron_variant		ENST00000304771.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MAP6	ENST00000304771.8	c.1120-124C>T		intron_variant		1	NM_033063.2	A2
MAP6	ENST00000434603.2	c.1120-124C>T		intron_variant		1		P2
MAP6	ENST00000526740.3	c.133-124C>T		intron_variant		5		A2

Frequencies

GnomAD3 genomes AF: 0.0856 AC: 13031 AN: 152166 Hom.: 766 Cov.: 32

Gnomad AFR AF: 0.0227

Gnomad AMI AF: 0.0877

Gnomad AMR AF: 0.0725

Gnomad ASJ AF: 0.168

Gnomad EAS AF: 0.00154

Gnomad SAS AF: 0.119

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.122

Gnomad OTH AF: 0.0826

GnomAD4 exome AF: 0.118 AC: 116715 AN: 986342 Hom.: 7537 AF XY: 0.119 AC XY: 59165 AN XY: 495476

Gnomad4 AFR exome AF: 0.0187

Gnomad4 AMR exome AF: 0.0524

Gnomad4 ASJ exome AF: 0.169

Gnomad4 EAS exome AF: 0.00155

Gnomad4 SAS exome AF: 0.126

Gnomad4 FIN exome AF: 0.106

Gnomad4 NFE exome AF: 0.128

Gnomad4 OTH exome AF: 0.110

GnomAD4 genome AF: 0.0855 AC: 13027 AN: 152284 Hom.: 763 Cov.: 32 AF XY: 0.0858 AC XY: 6389 AN XY: 74464

Gnomad4 AFR AF: 0.0226

Gnomad4 AMR AF: 0.0723

Gnomad4 ASJ AF: 0.168

Gnomad4 EAS AF: 0.00154

Gnomad4 SAS AF: 0.119

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.122

Gnomad4 OTH AF: 0.0818

Alfa AF: 0.0967 Hom.: 482

Bravo AF: 0.0791

Asia WGS AF: 0.0470 AC: 165 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jun 20, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	2.6
Dann	Benign	0.74

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: rs659463; hg19: chr11-75317173;