NM_005511.2:c.*444T>A

Variant names:

• chr9-5909152-T-A
• rs1056796
• NM_005511.2:c.*444T>A

Variant summary

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

The NM_005511.2(MLANA):​c.*444T>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: MLANA NM_005511.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.302
• Publications: 6 publications found

Genes affected

MLANA (HGNC:7124): (melan-A) Located in endoplasmic reticulum membrane; melanosome; and trans-Golgi network. [provided by Alliance of Genome Resources, Apr 2022]

BRD10 (HGNC:23378): (bromodomain containing 10)

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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MLANA	NM_005511.2	c.*444T>A		3_prime_UTR_variant	Exon 5 of 5	ENST00000381477.8	NP_005502.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MLANA	ENST00000381477.8	c.*444T>A		3_prime_UTR_variant	Exon 5 of 5	1	NM_005511.2	ENSP00000370886.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 7330 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 3936

African (AFR) AF: 0.00 AC: 0 AN: 122

American (AMR) AF: 0.00 AC: 0 AN: 746

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 130

East Asian (EAS) AF: 0.00 AC: 0 AN: 222

South Asian (SAS) AF: 0.00 AC: 0 AN: 556

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 200

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 32

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 4958

Other (OTH) AF: 0.00 AC: 0 AN: 364

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	2.6
DANN	Benign	0.86
PhyloP100		0.30

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: rs1056796; hg19: chr9-5909152;