rs7211770

Positions:

• chr17-40132750-A-G
• chr17-40132750-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.1489-292A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 152,060 control chromosomes in the GnomAD database, including 12,617 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 0.37 (12617 hom., cov: 32)
• Consequence: MSL1 NM_001365919.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.42

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MSL1	NM_001365919.1	c.1489-292A>G		intron_variant		ENST00000398532.9	NP_001352848.1
MSL1	NM_001365920.1	c.1441-292A>G		intron_variant			NP_001352849.1
MSL1	NM_001012241.2	c.700-292A>G		intron_variant			NP_001012241.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MSL1	ENST00000398532.9	c.1489-292A>G		intron_variant		1	NM_001365919.1	ENSP00000381543.3

Frequencies

GnomAD3 genomes AF: 0.368 AC: 55894 AN: 151942 Hom.: 12567 Cov.: 32

Gnomad AFR AF: 0.638

Gnomad AMI AF: 0.189

Gnomad AMR AF: 0.250

Gnomad ASJ AF: 0.258

Gnomad EAS AF: 0.310

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.356

Gnomad MID AF: 0.291

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.368 AC: 56002 AN: 152060 Hom.: 12617 Cov.: 32 AF XY: 0.366 AC XY: 27247 AN XY: 74350

Gnomad4 AFR AF: 0.639

Gnomad4 AMR AF: 0.251

Gnomad4 ASJ AF: 0.258

Gnomad4 EAS AF: 0.310

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.356

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.309

Alfa AF: 0.277 Hom.: 3787

Bravo AF: 0.372

Asia WGS AF: 0.298 AC: 1033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.0080
DANN	Benign	0.30

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: rs7211770; hg19: chr17-38289003;