rs11649339

Variant names:

• chr16-74238831-A-C
• rs11649339
• ENST00000562888.2:n.352-32666T>G

Variant summary

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

The ENST00000569389.5(PSMD7-DT):​n.130-32666T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.147 in 152,204 control chromosomes in the GnomAD database, including 1,649 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 0.15 (1649 hom., cov: 32)
• Consequence: PSMD7-DT ENST00000569389.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.374
• Publications: 4 publications found

Genes affected

PSMD7-DT (HGNC:53056): (PSMD7 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.5).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000569389.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PSMD7-DT	ENST00000562888.2	TSL:5	n.352-32666T>G		intron	N/A
	PSMD7-DT	ENST00000569389.5	TSL:3	n.130-32666T>G		intron	N/A
	PSMD7-DT	ENST00000641127.2		n.139-32666T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.147 AC: 22409 AN: 152086 Hom.: 1648 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.254

Gnomad AMR AF: 0.150

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.229

Gnomad SAS AF: 0.0745

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.147 AC: 22430 AN: 152204 Hom.: 1649 Cov.: 32 AF XY: 0.148 AC XY: 10996 AN XY: 74392

African (AFR) AF: 0.141 AC: 5876 AN: 41544

American (AMR) AF: 0.150 AC: 2300 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 711 AN: 3470

East Asian (EAS) AF: 0.228 AC: 1180 AN: 5168

South Asian (SAS) AF: 0.0742 AC: 358 AN: 4826

European-Finnish (FIN) AF: 0.201 AC: 2132 AN: 10594

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9293 AN: 68004

Other (OTH) AF: 0.147 AC: 309 AN: 2108

Alfa AF: 0.145 Hom.: 356

Bravo AF: 0.146

Asia WGS AF: 0.192 AC: 668 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.50
CADD	Benign	3.0
DANN	Benign	0.52
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs11649339; hg19: chr16-74272730;