2-188292236-T-G

Variant names:

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

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+70T>G variant causes a intron 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_016315.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.159
• 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]

ENSG00000310134 (HGNC:):

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=-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

African (AFR) AF: 0.500 AC: 3 AN: 6

American (AMR) AF: 0.00 AC: 0 AN: 2

Ashkenazi Jewish (ASJ) AF: 0.250 AC: 1 AN: 4

East Asian (EAS) AF: 0.100 AC: 1 AN: 10

South Asian (SAS) AF: 0.00 AC: 0 AN: 2

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 8

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 2

European-Non Finnish (NFE) AF: 0.159 AC: 34 AN: 214

Other (OTH) AF: 0.200 AC: 2 AN: 10

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

African (AFR) AF: 0.184 AC: 7633 AN: 41536

American (AMR) AF: 0.137 AC: 2090 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 385 AN: 3470

East Asian (EAS) AF: 0.0508 AC: 262 AN: 5154

South Asian (SAS) AF: 0.0728 AC: 351 AN: 4820

European-Finnish (FIN) AF: 0.162 AC: 1714 AN: 10610

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.156 AC: 10608 AN: 67990

Other (OTH) AF: 0.159 AC: 336 AN: 2116

Alfa AF: 0.144 Hom.: 2087

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
PhyloP100		0.16
PromoterAI		0.0018	Neutral
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: rs2004888; hg19: chr2-189156963;