rs9307241

Positions:

• chr4-99826007-C-T

Variant summary

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

The NM_014395.3(DAPP1):​c.101+8993C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0754 in 152,236 control chromosomes in the GnomAD database, including 501 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 0.075 (501 hom., cov: 32)
• Consequence: DAPP1 NM_014395.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190

Genes affected

DAPP1 (HGNC:16500): (dual adaptor of phosphotyrosine and 3-phosphoinositides 1) Enables phosphatidylinositol-3,4,5-trisphosphate binding activity and phosphatidylinositol-3,4-bisphosphate binding activity. Predicted to be involved in signal transduction. Located in plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.107 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
DAPP1	NM_014395.3	c.101+8993C>T		intron_variant		ENST00000512369.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
DAPP1	ENST00000512369.2	c.101+8993C>T		intron_variant		1	NM_014395.3	P1
DAPP1	ENST00000296414.11	c.101+8993C>T		intron_variant		1
DAPP1	ENST00000507994.1	n.165+8993C>T		intron_variant, non_coding_transcript_variant		2

Frequencies

GnomAD3 genomes AF: 0.0754 AC: 11473 AN: 152118 Hom.: 501 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0569

Gnomad ASJ AF: 0.0867

Gnomad EAS AF: 0.00481

Gnomad SAS AF: 0.0913

Gnomad FIN AF: 0.0812

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.0623

Gnomad OTH AF: 0.0770

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

GnomAD4 genome AF: 0.0754 AC: 11480 AN: 152236 Hom.: 501 Cov.: 32 AF XY: 0.0754 AC XY: 5612 AN XY: 74438

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.0569

Gnomad4 ASJ AF: 0.0867

Gnomad4 EAS AF: 0.00482

Gnomad4 SAS AF: 0.0914

Gnomad4 FIN AF: 0.0812

Gnomad4 NFE AF: 0.0622

Gnomad4 OTH AF: 0.0758

Alfa AF: 0.0650 Hom.: 714

Bravo AF: 0.0733

Asia WGS AF: 0.0570 AC: 200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.8
DANN	Benign	0.41

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs9307241; hg19: chr4-100747164;