rs6700586

chr1-37491775-G-A

Variant summary

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

The NM_001270875.3(MEAF6):c.*2324C>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 0.538 in 151,170 control chromosomes in the GnomAD database, including 23,021 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 0.54 (23021 hom., cov: 32)
• Consequence: MEAF6 NM_001270875.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.164

Genes affected

MEAF6 (HGNC:25674): (MYST/Esa1 associated factor 6) This gene encodes a nuclear protein involved in transcriptional activation. The encoded protein may form a component of several different histone acetyltransferase complexes. There is a pseudogene for this gene on chromosome 2. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2012]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.604 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MEAF6	NM_001270875.3	c.*2324C>T		3_prime_UTR_variant	7/7	ENST00000296214.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MEAF6	ENST00000296214.10	c.*2324C>T		3_prime_UTR_variant	7/7	1	NM_001270875.3	P4

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81243 AN: 151056 Hom.: 22988 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.601

Gnomad AMR AF: 0.594

Gnomad ASJ AF: 0.442

Gnomad EAS AF: 0.566

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.727

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.609

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.538 AC: 81315 AN: 151170 Hom.: 23021 Cov.: 32 AF XY: 0.542 AC XY: 40040 AN XY: 73872

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.595

Gnomad4 ASJ AF: 0.442

Gnomad4 EAS AF: 0.567

Gnomad4 SAS AF: 0.527

Gnomad4 FIN AF: 0.727

Gnomad4 NFE AF: 0.609

Gnomad4 OTH AF: 0.534

Alfa AF: 0.581 Hom.: 53142

Bravo AF: 0.519

Asia WGS AF: 0.604 AC: 2099 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.31
Dann	Benign	0.36

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6700586; hg19: chr1-37957376;