2-188427083-G-A

Variant names:

• chr2-188427083-G-A
• rs6714454
• NM_016315.4:c.-45+43194G>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.-45+43194G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0481 in 152,200 control chromosomes in the GnomAD database, including 335 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 0.048 (335 hom., cov: 32)
• Consequence: GULP1 NM_016315.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809
• 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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GULP1	NM_016315.4	c.-45+43194G>A		intron_variant	Intron 2 of 11	ENST00000409830.6	NP_057399.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GULP1	ENST00000409830.6	c.-45+43194G>A		intron_variant	Intron 2 of 11	1	NM_016315.4	ENSP00000386732.1

Frequencies

GnomAD3 genomes AF: 0.0482 AC: 7324 AN: 152084 Hom.: 337 Cov.: 32

Gnomad AFR AF: 0.0761

Gnomad AMI AF: 0.0848

Gnomad AMR AF: 0.0264

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.0107

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0222

Gnomad OTH AF: 0.0492

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

GnomAD4 genome AF: 0.0481 AC: 7319 AN: 152200 Hom.: 335 Cov.: 32 AF XY: 0.0508 AC XY: 3783 AN XY: 74418

African (AFR) AF: 0.0760 AC: 3156 AN: 41520

American (AMR) AF: 0.0263 AC: 402 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0337 AC: 117 AN: 3470

East Asian (EAS) AF: 0.197 AC: 1017 AN: 5156

South Asian (SAS) AF: 0.167 AC: 807 AN: 4820

European-Finnish (FIN) AF: 0.0107 AC: 114 AN: 10610

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0222 AC: 1510 AN: 68012

Other (OTH) AF: 0.0482 AC: 102 AN: 2116

Alfa AF: 0.0359 Hom.: 26

Bravo AF: 0.0494

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.43
PhyloP100		-0.81
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: rs6714454; hg19: chr2-189291810;