rs1354906

chr2-188582091-T-Cchr2-188582091-T-G

Variant summary

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

The NM_016315.4(GULP1):c.610-2174T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.663 in 151,898 control chromosomes in the GnomAD database, including 34,449 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 0.66 (34449 hom., cov: 31)
• Consequence: GULP1 NM_016315.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.749

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.891 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GULP1	NM_016315.4	c.610-2174T>C		intron_variant		ENST00000409830.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GULP1	ENST00000409830.6	c.610-2174T>C		intron_variant		1	NM_016315.4	P1

Frequencies

GnomAD3 genomes AF: 0.664 AC: 100719 AN: 151780 Hom.: 34446 Cov.: 31

Gnomad AFR AF: 0.494

Gnomad AMI AF: 0.908

Gnomad AMR AF: 0.750

Gnomad ASJ AF: 0.631

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.800

Gnomad FIN AF: 0.776

Gnomad MID AF: 0.780

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.691

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

GnomAD4 genome AF: 0.663 AC: 100748 AN: 151898 Hom.: 34449 Cov.: 31 AF XY: 0.671 AC XY: 49819 AN XY: 74252

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.750

Gnomad4 ASJ AF: 0.631

Gnomad4 EAS AF: 0.913

Gnomad4 SAS AF: 0.800

Gnomad4 FIN AF: 0.776

Gnomad4 NFE AF: 0.698

Gnomad4 OTH AF: 0.693

Alfa AF: 0.691 Hom.: 16650

Bravo AF: 0.655

Asia WGS AF: 0.821 AC: 2841 AN: 3466

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.53
Dann	Benign	0.58

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: rs1354906; hg19: chr2-189446818;