rs9307241

Variant names:

• chr4-99826007-C-T
• rs9307241
• NM_014395.3:c.101+8993C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014395.3. 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
	DAPP1	NM_014395.3	MANE Select	c.101+8993C>T		intron	N/A	NP_055210.2	Q9UN19-1
	DAPP1	NM_001306151.2		c.101+8993C>T		intron	N/A	NP_001293080.1	J3KNB3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	DAPP1	ENST00000512369.2	TSL:1 MANE Select	c.101+8993C>T		intron	N/A	ENSP00000423602.1	Q9UN19-1
	DAPP1	ENST00000296414.11	TSL:1	c.101+8993C>T		intron	N/A	ENSP00000296414.7	J3KNB3
	DAPP1	ENST00000851088.1		c.101+8993C>T		intron	N/A	ENSP00000521147.1

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

African (AFR) AF: 0.109 AC: 4536 AN: 41524

American (AMR) AF: 0.0569 AC: 870 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0867 AC: 301 AN: 3472

East Asian (EAS) AF: 0.00482 AC: 25 AN: 5186

South Asian (SAS) AF: 0.0914 AC: 441 AN: 4824

European-Finnish (FIN) AF: 0.0812 AC: 861 AN: 10606

Middle Eastern (MID) AF: 0.143 AC: 42 AN: 294

European-Non Finnish (NFE) AF: 0.0622 AC: 4231 AN: 68006

Other (OTH) AF: 0.0758 AC: 160 AN: 2112

Alfa AF: 0.0673 Hom.: 1206

Bravo AF: 0.0733

Asia WGS AF: 0.0570 AC: 200 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	5.8
DANN	Benign	0.41
PhyloP100		0.019
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9307241; hg19: chr4-100747164;