rs9610915

Variant names:

• chr22-38215073-C-A
• rs9610915
• NM_012323.4:c.*195C>A

Your query was ambiguous. Multiple possible variants found:

• chr22-38215073-C-A
• chr22-38215073-C-G

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_012323.4(MAFF):​c.*195C>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000522 in 383,226 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 31)
  • Exomes 𝑓: 0.0000052 (0 hom.)
• Consequence: MAFF NM_012323.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.490
• Publications: 10 publications found

Genes affected

MAFF (HGNC:6780): (MAF bZIP transcription factor F) The protein encoded by this gene is a basic leucine zipper (bZIP) transcription factor that lacks a transactivation domain. It is known to bind the US-2 DNA element in the promoter of the oxytocin receptor (OTR) gene and most likely heterodimerizes with other leucine zipper-containing proteins to enhance expression of the OTR gene during term pregnancy. The encoded protein can also form homodimers, and since it lacks a transactivation domain, the homodimer may act as a repressor of transcription. This gene may also be involved in the cellular stress response. Multiple transcript variants encoding two different isoforms have been found for this gene. [provided by RefSeq, Jun 2009]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_012323.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAFF	NM_012323.4	MANE Select	c.*195C>A		3_prime_UTR	Exon 3 of 3	NP_036455.1	Q9ULX9-1
	MAFF	NM_001161572.2		c.*195C>A		3_prime_UTR	Exon 3 of 3	NP_001155044.1	Q9ULX9-1
	MAFF	NM_001161573.1		c.*195C>A		3_prime_UTR	Exon 3 of 3	NP_001155045.1	Q9ULX9-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MAFF	ENST00000338483.7	TSL:1 MANE Select	c.*195C>A		3_prime_UTR	Exon 3 of 3	ENSP00000345393.2	Q9ULX9-1
	MAFF	ENST00000407965.2	TSL:2	c.*195C>A		3_prime_UTR	Exon 3 of 3	ENSP00000384094.1
	MAFF	ENST00000538320.5	TSL:4	c.*195C>A		3_prime_UTR	Exon 3 of 3	ENSP00000442060.1	Q9ULX9-1

Frequencies

GnomAD3 genomes Cov.: 31

GnomAD4 exome AF: 0.00000522 AC: 2 AN: 383226 Hom.: 0 Cov.: 4 AF XY: 0.00000489 AC XY: 1 AN XY: 204548

African (AFR) AF: 0.00 AC: 0 AN: 8010

American (AMR) AF: 0.00 AC: 0 AN: 12418

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 11324

East Asian (EAS) AF: 0.00 AC: 0 AN: 21934

South Asian (SAS) AF: 0.00 AC: 0 AN: 38030

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 43034

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3326

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 223494

Other (OTH) AF: 0.0000924 AC: 2 AN: 21656

GnomAD4 genome Cov.: 31

Alfa AF: 0.00 Hom.: 1871

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	6.1
DANN	Benign	0.79
PhyloP100		0.49
PromoterAI		0.023	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.0

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: rs9610915; hg19: chr22-38611080;