1-37493212-C-G

Variant names:

• chr1-37493212-C-G
• rs9253
• NM_001270875.3:c.*887G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001270875.3(MEAF6):​c.*887G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.13 in 152,134 control chromosomes in the GnomAD database, including 1,584 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 0.13 (1583 hom., cov: 33)
  • Exomes 𝑓: 0.089 (1 hom.)
• Consequence: MEAF6 NM_001270875.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.261
• Publications: 22 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MEAF6	NM_001270875.3	c.*887G>C		3_prime_UTR_variant	Exon 7 of 7	ENST00000296214.10	NP_001257804.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MEAF6	ENST00000296214.10	c.*887G>C		3_prime_UTR_variant	Exon 7 of 7	1	NM_001270875.3	ENSP00000296214.5

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19814 AN: 151892 Hom.: 1581 Cov.: 33

Gnomad AFR AF: 0.0414

Gnomad AMI AF: 0.199

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.174

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.0955

Gnomad NFE AF: 0.169

Gnomad OTH AF: 0.122

GnomAD4 exome AF: 0.0887 AC: 11 AN: 124 Hom.: 1 Cov.: 0 AF XY: 0.0526 AC XY: 4 AN XY: 76

African (AFR) AF: 0.00 AC: 0 AN: 2

American (AMR) AF: 0.00 AC: 0 AN: 4

Ashkenazi Jewish (ASJ) AF: 0.100 AC: 1 AN: 10

East Asian (EAS) AF: 0.00 AC: 0 AN: 6

South Asian (SAS) AF: 0.00 AC: 0 AN: 4

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.111 AC: 10 AN: 90

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.130 AC: 19821 AN: 152010 Hom.: 1583 Cov.: 33 AF XY: 0.132 AC XY: 9798 AN XY: 74292

African (AFR) AF: 0.0413 AC: 1711 AN: 41468

American (AMR) AF: 0.143 AC: 2188 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.129 AC: 447 AN: 3466

East Asian (EAS) AF: 0.174 AC: 899 AN: 5168

South Asian (SAS) AF: 0.175 AC: 842 AN: 4818

European-Finnish (FIN) AF: 0.167 AC: 1763 AN: 10536

Middle Eastern (MID) AF: 0.0959 AC: 28 AN: 292

European-Non Finnish (NFE) AF: 0.169 AC: 11504 AN: 67974

Other (OTH) AF: 0.122 AC: 258 AN: 2112

Alfa AF: 0.162 Hom.: 1183

Bravo AF: 0.123

Asia WGS AF: 0.181 AC: 629 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	5.8
DANN	Benign	0.77
PhyloP100		-0.26
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: rs9253; hg19: chr1-37958813;