rs1354905

Positions:

• chr2-188581744-G-A
• chr2-188581744-G-C

Variant summary

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

The NM_016315.4(GULP1):​c.610-2521G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.464 in 151,998 control chromosomes in the GnomAD database, including 17,051 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 0.46 (17051 hom., cov: 32)
• Consequence: GULP1 NM_016315.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.738

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=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.79 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GULP1	NM_016315.4	c.610-2521G>A		intron_variant		ENST00000409830.6	NP_057399.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GULP1	ENST00000409830.6	c.610-2521G>A		intron_variant		1	NM_016315.4	ENSP00000386732	P1

Frequencies

GnomAD3 genomes AF: 0.465 AC: 70580 AN: 151880 Hom.: 17052 Cov.: 32

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.523

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.810

Gnomad SAS AF: 0.650

Gnomad FIN AF: 0.486

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.464 AC: 70591 AN: 151998 Hom.: 17051 Cov.: 32 AF XY: 0.471 AC XY: 34967 AN XY: 74268

Gnomad4 AFR AF: 0.404

Gnomad4 AMR AF: 0.523

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.810

Gnomad4 SAS AF: 0.650

Gnomad4 FIN AF: 0.486

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.457

Alfa AF: 0.455 Hom.: 23535

Bravo AF: 0.465

Asia WGS AF: 0.666 AC: 2314 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.32
DANN	Benign	0.36

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: rs1354905; hg19: chr2-189446471;