rs2150702

Positions:

• chr9-5893861-G-A
• chr9-5893861-G-C
• 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>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.437 in 151,700 control chromosomes in the GnomAD database, including 14,953 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 0.44 (14953 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]

KIAA2026 (HGNC:23378): (bromodomain containing 10)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.492 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MLANA	ENST00000381477.8	c.77+1310G>A		intron_variant		1	NM_005511.2	P1

Frequencies

GnomAD3 genomes AF: 0.437 AC: 66183 AN: 151582 Hom.: 14948 Cov.: 29

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.580

Gnomad AMR AF: 0.413

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.179

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.447

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

GnomAD4 genome AF: 0.437 AC: 66230 AN: 151700 Hom.: 14953 Cov.: 29 AF XY: 0.430 AC XY: 31901 AN XY: 74170

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.412

Gnomad4 ASJ AF: 0.506

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.457

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.441

Alfa AF: 0.497 Hom.: 24625

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.9
DANN	Benign	0.76

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;