7-32700624-T-C

Position:

• chr7-32700624-T-C

Variant summary

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

The NR_036680.1(DPY19L1P1):​n.125+16094A>G variant causes a intron, non coding transcript 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 NR_036680.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DPY19L1P1	NR_036680.1	n.125+16094A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DPY19L1P1	ENST00000417811.2	n.826+16094A>G		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.820

Gnomad4 AMR AF: 0.938

Gnomad4 ASJ AF: 0.918

Gnomad4 EAS AF: 0.965

Gnomad4 SAS AF: 0.918

Gnomad4 FIN AF: 0.959

Gnomad4 NFE AF: 0.941

Gnomad4 OTH AF: 0.900

Alfa AF: 0.930 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	2.9
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs308480; hg19: chr7-32740236;