2-188434941-G-A

Variant names:

• chr2-188434941-G-A
• rs7595327
• NM_016315.4:c.-44-42718G>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.-44-42718G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 151,622 control chromosomes in the GnomAD database, including 7,540 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 0.28 (7540 hom., cov: 32)
• Consequence: GULP1 NM_016315.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570
• Publications: 1 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]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.496 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.-44-42718G>A		intron	N/A	NP_057399.1
	GULP1	NM_001375948.1		c.-44-42718G>A		intron	N/A	NP_001362877.1
	GULP1	NM_001375949.1		c.-138-31534G>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.-44-42718G>A		intron	N/A	ENSP00000386732.1
	GULP1	ENST00000359135.7	TSL:1	c.-44-42718G>A		intron	N/A	ENSP00000352047.3
	GULP1	ENST00000410051.5	TSL:1	c.-44-42718G>A		intron	N/A	ENSP00000387013.1

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43062 AN: 151500 Hom.: 7519 Cov.: 32

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.240

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.285 AC: 43150 AN: 151622 Hom.: 7540 Cov.: 32 AF XY: 0.282 AC XY: 20874 AN XY: 74100

African (AFR) AF: 0.502 AC: 20768 AN: 41360

American (AMR) AF: 0.195 AC: 2972 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 638 AN: 3470

East Asian (EAS) AF: 0.267 AC: 1374 AN: 5150

South Asian (SAS) AF: 0.247 AC: 1187 AN: 4810

European-Finnish (FIN) AF: 0.175 AC: 1836 AN: 10500

Middle Eastern (MID) AF: 0.250 AC: 73 AN: 292

European-Non Finnish (NFE) AF: 0.199 AC: 13508 AN: 67798

Other (OTH) AF: 0.272 AC: 573 AN: 2110

Alfa AF: 0.126 Hom.: 217

Bravo AF: 0.294

Asia WGS AF: 0.285 AC: 984 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.6
DANN	Benign	0.16
PhyloP100		0.057
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: rs7595327; hg19: chr2-189299668;