rs10512482

Variant names:

• chr17-40132808-A-T
• rs10512482
• NM_001365919.1:c.1489-234A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001365919.1(MSL1):​c.1489-234A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0796 in 152,186 control chromosomes in the GnomAD database, including 1,134 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 0.080 (1134 hom., cov: 32)
• Consequence: MSL1 NM_001365919.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.144
• Publications: 3 publications found

Genes affected

MSL1 (HGNC:27905): (MSL complex subunit 1) Predicted to enable chromatin binding activity. Involved in histone H4-K16 acetylation. Located in nucleoplasm. Part of MSL complex. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000310351 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.22 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001365919.1. 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
	MSL1	NM_001365919.1	MANE Select	c.1489-234A>T		intron	N/A	NP_001352848.1
	MSL1	NM_001365920.1		c.1441-234A>T		intron	N/A	NP_001352849.1
	MSL1	NM_001012241.2		c.700-234A>T		intron	N/A	NP_001012241.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MSL1	ENST00000398532.9	TSL:1 MANE Select	c.1489-234A>T		intron	N/A	ENSP00000381543.3
	MSL1	ENST00000579565.5	TSL:1	c.700-234A>T		intron	N/A	ENSP00000462945.1
	MSL1	ENST00000578648.5	TSL:5	c.1441-234A>T		intron	N/A	ENSP00000462731.1

Frequencies

GnomAD3 genomes AF: 0.0794 AC: 12075 AN: 152068 Hom.: 1121 Cov.: 32

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0435

Gnomad ASJ AF: 0.00979

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00559

Gnomad FIN AF: 0.0231

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0253

Gnomad OTH AF: 0.0626

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

GnomAD4 genome AF: 0.0796 AC: 12121 AN: 152186 Hom.: 1134 Cov.: 32 AF XY: 0.0781 AC XY: 5813 AN XY: 74408

African (AFR) AF: 0.224 AC: 9285 AN: 41480

American (AMR) AF: 0.0433 AC: 662 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.00979 AC: 34 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5192

South Asian (SAS) AF: 0.00559 AC: 27 AN: 4830

European-Finnish (FIN) AF: 0.0231 AC: 245 AN: 10604

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0253 AC: 1723 AN: 68010

Other (OTH) AF: 0.0620 AC: 131 AN: 2114

Alfa AF: 0.0551 Hom.: 92

Bravo AF: 0.0875

Asia WGS AF: 0.0230 AC: 79 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.4
DANN	Benign	0.88
PhyloP100		0.14
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: rs10512482; hg19: chr17-38289061;