chr2-188311178-G-A

Variant names:

• chr2-188311178-G-A
• rs11688935
• NM_016315.4:c.-172+19012G>A

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+19012G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.753 in 152,104 control chromosomes in the GnomAD database, including 43,530 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 0.75 (43530 hom., cov: 32)
• Consequence: GULP1 NM_016315.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32
• Publications: 6 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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.929 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GULP1	NM_016315.4	MANE Select	c.-172+19012G>A		intron	N/A	NP_057399.1
	GULP1	NM_001375948.1		c.-172+19012G>A		intron	N/A	NP_001362877.1
	GULP1	NM_001375949.1		c.-266+18066G>A		intron	N/A	NP_001362878.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GULP1	ENST00000409830.6	TSL:1 MANE Select	c.-172+19012G>A		intron	N/A	ENSP00000386732.1
	GULP1	ENST00000359135.7	TSL:1	c.-172+18066G>A		intron	N/A	ENSP00000352047.3
	GULP1	ENST00000410051.5	TSL:1	c.-172+19012G>A		intron	N/A	ENSP00000387013.1

Frequencies

GnomAD3 genomes AF: 0.753 AC: 114370 AN: 151986 Hom.: 43486 Cov.: 32

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.758

Gnomad AMR AF: 0.805

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.951

Gnomad SAS AF: 0.713

Gnomad FIN AF: 0.733

Gnomad MID AF: 0.726

Gnomad NFE AF: 0.693

Gnomad OTH AF: 0.766

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

GnomAD4 genome AF: 0.753 AC: 114475 AN: 152104 Hom.: 43530 Cov.: 32 AF XY: 0.755 AC XY: 56144 AN XY: 74362

African (AFR) AF: 0.827 AC: 34319 AN: 41504

American (AMR) AF: 0.805 AC: 12311 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2124 AN: 3472

East Asian (EAS) AF: 0.951 AC: 4921 AN: 5176

South Asian (SAS) AF: 0.714 AC: 3434 AN: 4812

European-Finnish (FIN) AF: 0.733 AC: 7750 AN: 10576

Middle Eastern (MID) AF: 0.736 AC: 215 AN: 292

European-Non Finnish (NFE) AF: 0.693 AC: 47088 AN: 67964

Other (OTH) AF: 0.768 AC: 1623 AN: 2114

Alfa AF: 0.721 Hom.: 10059

Bravo AF: 0.766

Asia WGS AF: 0.838 AC: 2913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.011
DANN	Benign	0.54
PhyloP100		-1.3
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: rs11688935; hg19: chr2-189175905;