chr22-36398139-G-A

Variant names:

• chr22-36398139-G-A
• rs738278
• NR_183572.1:n.2164G>A

Variant summary

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

The NR_183572.1(MYH9-DT):​n.2164G>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_183572.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.838
• Publications: 7 publications found

Genes affected

MYH9-DT (HGNC:55867): (MYH9 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_183572.1. 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
	MYH9-DT	NR_183572.1		n.2164G>A		non_coding_transcript_exon	Exon 2 of 2
	MYH9-DT	NR_183574.1		n.2239G>A		non_coding_transcript_exon	Exon 3 of 3
	MYH9-DT	NR_183573.1		n.240+1924G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MYH9-DT	ENST00000737605.1		n.263+1924G>A		intron	N/A
	MYH9-DT	ENST00000737606.1		n.458+1924G>A		intron	N/A
	MYH9-DT	ENST00000737607.1		n.451+1914G>A		intron	N/A

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

African (AFR) AF: 0.0915 AC: 3797 AN: 41484

American (AMR) AF: 0.0362 AC: 552 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.0554 AC: 192 AN: 3468

East Asian (EAS) AF: 0.103 AC: 530 AN: 5164

South Asian (SAS) AF: 0.0305 AC: 147 AN: 4816

European-Finnish (FIN) AF: 0.0718 AC: 759 AN: 10570

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0524 AC: 3563 AN: 67968

Other (OTH) AF: 0.0479 AC: 101 AN: 2110

Alfa AF: 0.0462 Hom.: 101

Bravo AF: 0.0625

Asia WGS AF: 0.0810 AC: 281 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.091
DANN	Benign	0.25
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs738278; hg19: chr22-36794184;