7-32700624-T-G

Variant names:

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

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000417811.2(DPY19L1P1):​n.826+16094A>C 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 0.0000093 (0 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: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DPY19L1P1	NR_036680.1	n.125+16094A>C		intron_variant	Intron 2 of 16

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
DPY19L1P1	ENST00000417811.2	n.826+16094A>C		intron_variant	Intron 7 of 21	6
ENSG00000293957	ENST00000720109.1	n.449-21494A>C		intron_variant	Intron 4 of 12
ENSG00000293957	ENST00000720110.1	n.420-21494A>C		intron_variant	Intron 4 of 16

Frequencies

GnomAD3 genomes AF: 0.00000932 AC: 1 AN: 107292 Hom.: 0 Cov.: 15

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0000997

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.00000932 AC: 1 AN: 107292 Hom.: 0 Cov.: 15 AF XY: 0.0000197 AC XY: 1 AN XY: 50712

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.00 AC: 0 AN: 28646

American (AMR) AF: 0.0000997 AC: 1 AN: 10028

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2642

East Asian (EAS) AF: 0.00 AC: 0 AN: 3702

South Asian (SAS) AF: 0.00 AC: 0 AN: 2748

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 6782

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 264

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 50424

Other (OTH) AF: 0.00 AC: 0 AN: 1368

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 1972

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	2.6
DANN	Benign	0.47

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;