17-40132808-A-T

Position:

• chr17-40132808-A-T

Variant summary

Our verdict is Benign. Variant got -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

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]

MSL1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MSL1	NM_001365919.1	c.1489-234A>T		intron_variant		ENST00000398532.9	NP_001352848.1
MSL1	NM_001365920.1	c.1441-234A>T		intron_variant			NP_001352849.1
MSL1	NM_001012241.2	c.700-234A>T		intron_variant			NP_001012241.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MSL1	ENST00000398532.9	c.1489-234A>T		intron_variant		1	NM_001365919.1	ENSP00000381543.3

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

Gnomad4 AFR AF: 0.224

Gnomad4 AMR AF: 0.0433

Gnomad4 ASJ AF: 0.00979

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00559

Gnomad4 FIN AF: 0.0231

Gnomad4 NFE AF: 0.0253

Gnomad4 OTH AF: 0.0620

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.4
DANN	Benign	0.88

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: rs10512482; hg19: chr17-38289061;