rs7211770

Variant names:

• chr17-40132750-A-G
• rs7211770
• NM_001365919.1:c.1489-292A>G

Your query was ambiguous. Multiple possible variants found:

• chr17-40132750-A-G
• chr17-40132750-A-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.1489-292A>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
• Publications: 9 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.632 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.1489-292A>G		intron	N/A	NP_001352848.1
	MSL1	NM_001365920.1		c.1441-292A>G		intron	N/A	NP_001352849.1
	MSL1	NM_001012241.2		c.700-292A>G		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.1489-292A>G		intron	N/A	ENSP00000381543.3
	MSL1	ENST00000579565.5	TSL:1	c.700-292A>G		intron	N/A	ENSP00000462945.1
	MSL1	ENST00000578648.5	TSL:5	c.1441-292A>G		intron	N/A	ENSP00000462731.1

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

African (AFR) AF: 0.639 AC: 26451 AN: 41424

American (AMR) AF: 0.251 AC: 3835 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.258 AC: 896 AN: 3472

East Asian (EAS) AF: 0.310 AC: 1604 AN: 5178

South Asian (SAS) AF: 0.195 AC: 939 AN: 4824

European-Finnish (FIN) AF: 0.356 AC: 3760 AN: 10568

Middle Eastern (MID) AF: 0.293 AC: 86 AN: 294

European-Non Finnish (NFE) AF: 0.259 AC: 17605 AN: 67984

Other (OTH) AF: 0.309 AC: 654 AN: 2116

Alfa AF: 0.290 Hom.: 6015

Bravo AF: 0.372

Asia WGS AF: 0.298 AC: 1033 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.0080
DANN	Benign	0.30
PhyloP100		-2.4
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: rs7211770; hg19: chr17-38289003;