9-5893861-G-T

Variant names:

• chr9-5893861-G-T
• rs2150702
• NM_005511.2:c.77+1310G>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 30 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: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_005511.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MLANA	NM_005511.2	MANE Select	c.77+1310G>T		intron	N/A	NP_005502.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MLANA	ENST00000381477.8	TSL:1 MANE Select	c.77+1310G>T		intron	N/A	ENSP00000370886.3
	MLANA	ENST00000381471.1	TSL:2	c.77+1310G>T		intron	N/A	ENSP00000370880.1
	MLANA	ENST00000381476.5	TSL:3	c.77+1310G>T		intron	N/A	ENSP00000370885.1

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

African (AFR) AF: 0.193 AC: 7962 AN: 41324

American (AMR) AF: 0.0285 AC: 435 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.0444 AC: 154 AN: 3468

East Asian (EAS) AF: 0.203 AC: 1043 AN: 5150

South Asian (SAS) AF: 0.0779 AC: 375 AN: 4816

European-Finnish (FIN) AF: 0.0205 AC: 216 AN: 10512

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.00926 AC: 629 AN: 67938

Other (OTH) AF: 0.0653 AC: 138 AN: 2114

Alfa AF: 0.000249 Hom.: 39152

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.4
DANN	Benign	0.80
PhyloP100		0.0010
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: rs2150702; hg19: chr9-5893861;