chr2-188308570-C-G

Variant names:

• chr2-188308570-C-G
• rs4413123
• NM_016315.4:c.-172+16404C>G

Variant summary

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

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]

LINC01090 (HGNC:49201): (long intergenic non-protein coding RNA 1090)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016315.4. 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
	GULP1	NM_016315.4	MANE Select	c.-172+16404C>G		intron	N/A	NP_057399.1	Q9UBP9-1
	GULP1	NM_001375948.1		c.-172+16404C>G		intron	N/A	NP_001362877.1	H7BZV7
	GULP1	NM_001375949.1		c.-266+15458C>G		intron	N/A	NP_001362878.1	H7BZV7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GULP1	ENST00000409830.6	TSL:1 MANE Select	c.-172+16404C>G		intron	N/A	ENSP00000386732.1	Q9UBP9-1
	GULP1	ENST00000359135.7	TSL:1	c.-172+15458C>G		intron	N/A	ENSP00000352047.3	Q9UBP9-1
	GULP1	ENST00000410051.5	TSL:1	c.-172+16404C>G		intron	N/A	ENSP00000387013.1	Q9UBP9-2

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

African (AFR) AF: 0.648 AC: 26865 AN: 41442

American (AMR) AF: 0.669 AC: 10227 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.501 AC: 1737 AN: 3468

East Asian (EAS) AF: 0.899 AC: 4625 AN: 5142

South Asian (SAS) AF: 0.640 AC: 3074 AN: 4802

European-Finnish (FIN) AF: 0.571 AC: 6014 AN: 10538

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.537 AC: 36464 AN: 67942

Other (OTH) AF: 0.610 AC: 1290 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.16
PhyloP100		-2.0
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: rs4413123; hg19: chr2-189173297;