7-32700624-T-C

Variant names:

• chr7-32700624-T-C
• rs308480
• ENST00000417811.2:n.826+16094A>G

Variant summary

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

The ENST00000417811.2(DPY19L1P1):​n.826+16094A>G variant causes a intron change. 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 0.91 (44100 hom., cov: 15)
• Consequence: DPY19L1P1 ENST00000417811.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 2 publications found

Genes affected

DPY19L1P1 (HGNC:22395): (DPY19L1 pseudogene 1)

ENSG00000293957 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000417811.2. 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
	DPY19L1P1	NR_036680.1		n.125+16094A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DPY19L1P1	ENST00000417811.2	TSL:6	n.826+16094A>G		intron	N/A
	ENSG00000293957	ENST00000720109.1		n.449-21494A>G		intron	N/A
	ENSG00000293957	ENST00000720110.1		n.420-21494A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.909 AC: 97329 AN: 107072 Hom.: 44076 Cov.: 15

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.938

Gnomad ASJ AF: 0.918

Gnomad EAS AF: 0.965

Gnomad SAS AF: 0.918

Gnomad FIN AF: 0.959

Gnomad MID AF: 0.970

Gnomad NFE AF: 0.941

Gnomad OTH AF: 0.898

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

GnomAD4 genome AF: 0.909 AC: 97390 AN: 107148 Hom.: 44100 Cov.: 15 AF XY: 0.906 AC XY: 45941 AN XY: 50688

African (AFR) AF: 0.820 AC: 23426 AN: 28574

American (AMR) AF: 0.938 AC: 9407 AN: 10028

Ashkenazi Jewish (ASJ) AF: 0.918 AC: 2425 AN: 2642

East Asian (EAS) AF: 0.965 AC: 3558 AN: 3688

South Asian (SAS) AF: 0.918 AC: 2514 AN: 2738

European-Finnish (FIN) AF: 0.959 AC: 6505 AN: 6780

Middle Eastern (MID) AF: 0.963 AC: 235 AN: 244

European-Non Finnish (NFE) AF: 0.941 AC: 47403 AN: 50380

Other (OTH) AF: 0.900 AC: 1247 AN: 1386

Alfa AF: 0.930 Hom.: 1972

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.9
DANN	Benign	0.59
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs308480; hg19: chr7-32740236;