chr1-39230975-G-A

Position:

• chr1-39230975-G-A

Variant summary

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

The NM_001394062.1(MACF1):​c.110-207G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.964 in 152,266 control chromosomes in the GnomAD database, including 70,856 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency: Genomes: 𝑓 0.96 (70856 hom., cov: 31)
• Consequence: MACF1 NM_001394062.1 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -1.21

Genes affected

MACF1 (HGNC:13664): (microtubule actin crosslinking factor 1) This gene encodes a large protein containing numerous spectrin and leucine-rich repeat (LRR) domains. The encoded protein is a member of a family of proteins that form bridges between different cytoskeletal elements. This protein facilitates actin-microtubule interactions at the cell periphery and couples the microtubule network to cellular junctions. Alternative splicing results in multiple transcript variants, but the full-length nature of some of these variants has not been determined. [provided by RefSeq, May 2013]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BP6: Variant 1-39230975-G-A is Benign according to our data. Variant chr1-39230975-G-A is described in ClinVar as [Benign]. Clinvar id is 1265512.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.99 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MACF1	NM_001394062.1	c.110-207G>A		intron_variant		ENST00000564288.6	NP_001380991.1
MACF1	NM_012090.5	c.221-207G>A		intron_variant			NP_036222.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MACF1	ENST00000564288.6	c.110-207G>A		intron_variant		5	NM_001394062.1	ENSP00000455274
	ENST00000669616.1	n.75-2439C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.964 AC: 146647 AN: 152148 Hom.: 70831 Cov.: 31

Gnomad AFR AF: 0.888

Gnomad AMI AF: 0.969

Gnomad AMR AF: 0.980

Gnomad ASJ AF: 0.983

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.996

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.996

Gnomad OTH AF: 0.968

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.964 AC: 146725 AN: 152266 Hom.: 70856 Cov.: 31 AF XY: 0.964 AC XY: 71784 AN XY: 74454

Gnomad4 AFR AF: 0.887

Gnomad4 AMR AF: 0.980

Gnomad4 ASJ AF: 0.983

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.996

Gnomad4 FIN AF: 0.997

Gnomad4 NFE AF: 0.996

Gnomad4 OTH AF: 0.964

Alfa AF: 0.979 Hom.: 8518

Bravo AF: 0.960

Asia WGS AF: 0.945 AC: 3286 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

May 12, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.26
DANN	Benign	0.72

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs2490951; hg19: chr1-39696647;