chr2-188292236-T-G

Variant names:

• chr2-188292236-T-G
• rs2004888
• NM_016315.4:c.-172+70T>G

Variant summary

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

The NM_001375936.1(GULP1):​c.-547T>G variant causes a 5 prime UTR premature start codon gain change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,468 control chromosomes in the GnomAD database, including 1,972 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 0.15 (1969 hom., cov: 33)
  • Exomes 𝑓: 0.16 (3 hom.)
• Consequence: GULP1 NM_001375936.1 5_prime_UTR_premature_start_codon_gain
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.159

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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GULP1	NM_016315.4	c.-172+70T>G		intron_variant	Intron 1 of 11	ENST00000409830.6	NP_057399.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GULP1	ENST00000409830.6	c.-172+70T>G		intron_variant	Intron 1 of 11	1	NM_016315.4	ENSP00000386732.1

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23531 AN: 152092 Hom.: 1964 Cov.: 33

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.158

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.0507

Gnomad SAS AF: 0.0732

Gnomad FIN AF: 0.162

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.156

Gnomad OTH AF: 0.151

GnomAD4 exome AF: 0.159 AC: 41 AN: 258 Hom.: 3 Cov.: 0 AF XY: 0.160 AC XY: 33 AN XY: 206

Gnomad4 AFR exome AF: 0.500

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.250

Gnomad4 EAS exome AF: 0.100

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.159

Gnomad4 OTH exome AF: 0.200

GnomAD4 genome AF: 0.155 AC: 23573 AN: 152210 Hom.: 1969 Cov.: 33 AF XY: 0.153 AC XY: 11359 AN XY: 74410

Gnomad4 AFR AF: 0.184

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.111

Gnomad4 EAS AF: 0.0508

Gnomad4 SAS AF: 0.0728

Gnomad4 FIN AF: 0.162

Gnomad4 NFE AF: 0.156

Gnomad4 OTH AF: 0.159

Alfa AF: 0.139 Hom.: 1513

Bravo AF: 0.153

Asia WGS AF: 0.0930 AC: 324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	6.2
DANN	Benign	0.47

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: rs2004888; hg19: chr2-189156963;