2-188294042-A-G

Position:

• chr2-188294042-A-G

Variant summary

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

The ENST00000409830.6(GULP1):​c.-172+1876A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 152,092 control chromosomes in the GnomAD database, including 24,508 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 0.56 (24498 hom., cov: 33)
  • Exomes 𝑓: 0.60 (10 hom.)
• Consequence: GULP1 ENST00000409830.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.893

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]

GULP1 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GULP1	NM_016315.4	c.-172+1876A>G		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+1876A>G		intron_variant		1	NM_016315.4	ENSP00000386732.1

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85365 AN: 151922 Hom.: 24500 Cov.: 33

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.587

GnomAD4 exome AF: 0.596 AC: 31 AN: 52 Hom.: 10 Cov.: 0 AF XY: 0.550 AC XY: 22 AN XY: 40

Gnomad4 EAS exome AF: 1.00

Gnomad4 FIN exome AF: 0.750

Gnomad4 NFE exome AF: 0.565

GnomAD4 genome AF: 0.562 AC: 85407 AN: 152040 Hom.: 24498 Cov.: 33 AF XY: 0.567 AC XY: 42144 AN XY: 74302

Gnomad4 AFR AF: 0.554

Gnomad4 AMR AF: 0.654

Gnomad4 ASJ AF: 0.488

Gnomad4 EAS AF: 0.895

Gnomad4 SAS AF: 0.633

Gnomad4 FIN AF: 0.567

Gnomad4 NFE AF: 0.517

Gnomad4 OTH AF: 0.582

Alfa AF: 0.531 Hom.: 11526

Bravo AF: 0.574

Asia WGS AF: 0.730 AC: 2537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	13
DANN	Benign	0.61

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: rs6753371; hg19: chr2-189158769;