9-5893861-G-T

Position:

• chr9-5893861-G-T

Variant summary

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

The NM_005511.2(MLANA):​c.77+1310G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0722 in 151,770 control chromosomes in the GnomAD database, including 929 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 0.072 (929 hom., cov: 29)
• Consequence: MLANA NM_005511.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00100

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)

MLANA (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MLANA	NM_005511.2	c.77+1310G>T		intron_variant		ENST00000381477.8	NP_005502.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MLANA	ENST00000381477.8	c.77+1310G>T		intron_variant		1	NM_005511.2	ENSP00000370886.3

Frequencies

GnomAD3 genomes AF: 0.0721 AC: 10931 AN: 151650 Hom.: 926 Cov.: 29

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0286

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.0782

Gnomad FIN AF: 0.0205

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00926

Gnomad OTH AF: 0.0626

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

GnomAD4 genome AF: 0.0722 AC: 10961 AN: 151770 Hom.: 929 Cov.: 29 AF XY: 0.0738 AC XY: 5477 AN XY: 74206

Gnomad4 AFR AF: 0.193

Gnomad4 AMR AF: 0.0285

Gnomad4 ASJ AF: 0.0444

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.0779

Gnomad4 FIN AF: 0.0205

Gnomad4 NFE AF: 0.00926

Gnomad4 OTH AF: 0.0653

Alfa AF: 0.000393 Hom.: 24625

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.4
DANN	Benign	0.80

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

Publications

LitVar

Other links and lift over

dbSNP: rs2150702; hg19: chr9-5893861;