rs738278

chr22-36398139-G-Achr22-36398139-G-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_183574.1(MYH9-DT):n.2239G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0638 in 152,044 control chromosomes in the GnomAD database, including 350 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 0.064 (350 hom., cov: 31)
• Consequence: MYH9-DT NR_183574.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.838

Genes affected

MYH9-DT (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0954 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MYH9-DT	NR_183574.1	n.2239G>A		non_coding_transcript_exon_variant	3/3
MYH9-DT	NR_183572.1	n.2164G>A		non_coding_transcript_exon_variant	2/2
MYH9-DT	NR_183573.1	n.240+1924G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0637 AC: 9680 AN: 151926 Hom.: 348 Cov.: 31

Gnomad AFR AF: 0.0913

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0362

Gnomad ASJ AF: 0.0554

Gnomad EAS AF: 0.104

Gnomad SAS AF: 0.0311

Gnomad FIN AF: 0.0718

Gnomad MID AF: 0.0285

Gnomad NFE AF: 0.0524

Gnomad OTH AF: 0.0469

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

GnomAD4 genome AF: 0.0638 AC: 9693 AN: 152044 Hom.: 350 Cov.: 31 AF XY: 0.0631 AC XY: 4686 AN XY: 74310

Gnomad4 AFR AF: 0.0915

Gnomad4 AMR AF: 0.0362

Gnomad4 ASJ AF: 0.0554

Gnomad4 EAS AF: 0.103

Gnomad4 SAS AF: 0.0305

Gnomad4 FIN AF: 0.0718

Gnomad4 NFE AF: 0.0524

Gnomad4 OTH AF: 0.0479

Alfa AF: 0.0448 Hom.: 86

Bravo AF: 0.0625

Asia WGS AF: 0.0810 AC: 281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
Cadd	Benign	0.091
Dann	Benign	0.25

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs738278; hg19: chr22-36794184;