chr2-188595826-T-C

Position:

• chr2-188595826-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_016315.4(GULP1):​c.*1815T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.81 in 152,070 control chromosomes in the GnomAD database, including 51,194 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 0.81 (51022 hom., cov: 32)
  • Exomes 𝑓: 0.89 (172 hom.)
• Consequence: GULP1 NM_016315.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274

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

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GULP1	NM_016315.4	c.*1815T>C		3_prime_UTR_variant	12/12	ENST00000409830.6	NP_057399.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GULP1	ENST00000409830.6	c.*1815T>C		3_prime_UTR_variant	12/12	1	NM_016315.4	ENSP00000386732.1
GULP1	ENST00000359135.7	c.*1815T>C		3_prime_UTR_variant	12/12	1		ENSP00000352047.3
GULP1	ENST00000699998.1	c.*1815T>C		3_prime_UTR_variant	13/13			ENSP00000514748.1
GULP1	ENST00000409580.5	c.*1815T>C		3_prime_UTR_variant	13/13	2		ENSP00000386289.1

Frequencies

GnomAD3 genomes AF: 0.810 AC: 122674 AN: 151522 Hom.: 51012 Cov.: 32

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.950

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.968

Gnomad FIN AF: 0.904

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.839

GnomAD4 exome AF: 0.887 AC: 383 AN: 432 Hom.: 172 Cov.: 0 AF XY: 0.888 AC XY: 231 AN XY: 260

Gnomad4 FIN exome AF: 0.887

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.809 AC: 122722 AN: 151638 Hom.: 51022 Cov.: 32 AF XY: 0.813 AC XY: 60230 AN XY: 74108

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.854

Gnomad4 ASJ AF: 0.844

Gnomad4 EAS AF: 0.960

Gnomad4 SAS AF: 0.968

Gnomad4 FIN AF: 0.904

Gnomad4 NFE AF: 0.886

Gnomad4 OTH AF: 0.841

Alfa AF: 0.865 Hom.: 65282

Bravo AF: 0.794

Asia WGS AF: 0.937 AC: 3244 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	11
DANN	Benign	0.77

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs8273; hg19: chr2-189460553;