2-188311178-G-A

Position:

• chr2-188311178-G-A

Variant summary

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

The ENST00000409830.6(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 ENST00000409830.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.32

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GULP1	NM_016315.4	c.-172+19012G>A		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+19012G>A		intron_variant		1	NM_016315.4	ENSP00000386732	P1

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

Gnomad4 AFR AF: 0.827

Gnomad4 AMR AF: 0.805

Gnomad4 ASJ AF: 0.612

Gnomad4 EAS AF: 0.951

Gnomad4 SAS AF: 0.714

Gnomad4 FIN AF: 0.733

Gnomad4 NFE AF: 0.693

Gnomad4 OTH AF: 0.768

Alfa AF: 0.719 Hom.: 9819

Bravo AF: 0.766

Asia WGS AF: 0.838 AC: 2913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.011
DANN	Benign	0.54

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: rs11688935; hg19: chr2-189175905;