chr1-37491775-G-A

Variant names:

• chr1-37491775-G-A
• rs6700586
• NM_001270875.3:c.*2324C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 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=-0.99).
• 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 rank	MANE	Protein	UniProt
MEAF6	NM_001270875.3	c.*2324C>T		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.*2324C>T		3_prime_UTR_variant	Exon 7 of 7	1	NM_001270875.3	ENSP00000296214.5

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

African (AFR) AF: 0.359 AC: 14797 AN: 41262

American (AMR) AF: 0.595 AC: 9045 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.442 AC: 1535 AN: 3470

East Asian (EAS) AF: 0.567 AC: 2921 AN: 5154

South Asian (SAS) AF: 0.527 AC: 2539 AN: 4818

European-Finnish (FIN) AF: 0.727 AC: 7370 AN: 10136

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.609 AC: 41338 AN: 67838

Other (OTH) AF: 0.534 AC: 1117 AN: 2092

Alfa AF: 0.572 Hom.: 81302

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
PhyloP100		-0.16

Splicing

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

Other links and lift over

dbSNP: rs6700586; hg19: chr1-37957376;