rs4413123

Positions:

• chr2-188308570-C-G
• chr2-188308570-C-T

Variant summary

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

The NM_016315.4(GULP1):​c.-172+16404C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.599 in 151,926 control chromosomes in the GnomAD database, including 27,814 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 0.60 (27814 hom., cov: 32)
• Consequence: GULP1 NM_016315.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.00

Genes affected

GULP1 (HGNC:18649): (GULP PTB domain containing engulfment adaptor 1) The protein encoded by this gene is an adapter protein necessary for the engulfment of apoptotic cells by phagocytes. Several transcript variants, some protein coding and some thought not to be protein coding, have been found for this gene. [provided by RefSeq, Nov 2011]

GULP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.878 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GULP1	NM_016315.4	c.-172+16404C>G		intron_variant		ENST00000409830.6	NP_057399.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GULP1	ENST00000409830.6	c.-172+16404C>G		intron_variant		1	NM_016315.4	ENSP00000386732.1

Frequencies

GnomAD3 genomes AF: 0.599 AC: 90947 AN: 151810 Hom.: 27805 Cov.: 32

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.501

Gnomad EAS AF: 0.900

Gnomad SAS AF: 0.640

Gnomad FIN AF: 0.571

Gnomad MID AF: 0.563

Gnomad NFE AF: 0.537

Gnomad OTH AF: 0.616

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

GnomAD4 genome AF: 0.599 AC: 91006 AN: 151926 Hom.: 27814 Cov.: 32 AF XY: 0.604 AC XY: 44800 AN XY: 74228

Gnomad4 AFR AF: 0.648

Gnomad4 AMR AF: 0.669

Gnomad4 ASJ AF: 0.501

Gnomad4 EAS AF: 0.899

Gnomad4 SAS AF: 0.640

Gnomad4 FIN AF: 0.571

Gnomad4 NFE AF: 0.537

Gnomad4 OTH AF: 0.610

Alfa AF: 0.559 Hom.: 2981

Bravo AF: 0.615

Asia WGS AF: 0.743 AC: 2582 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.16

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: rs4413123; hg19: chr2-189173297;