rs6714454

Positions:

• chr2-188427083-G-A

Variant summary

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

The NM_016315.4(GULP1):​c.-45+43194G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0481 in 152,200 control chromosomes in the GnomAD database, including 335 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 0.048 (335 hom., cov: 32)
• Consequence: GULP1 NM_016315.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.809

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=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.187 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GULP1	NM_016315.4	c.-45+43194G>A		intron_variant		ENST00000409830.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GULP1	ENST00000409830.6	c.-45+43194G>A		intron_variant		1	NM_016315.4	P1

Frequencies

GnomAD3 genomes AF: 0.0482 AC: 7324 AN: 152084 Hom.: 337 Cov.: 32

Gnomad AFR AF: 0.0761

Gnomad AMI AF: 0.0848

Gnomad AMR AF: 0.0264

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.197

Gnomad SAS AF: 0.168

Gnomad FIN AF: 0.0107

Gnomad MID AF: 0.0601

Gnomad NFE AF: 0.0222

Gnomad OTH AF: 0.0492

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

GnomAD4 genome AF: 0.0481 AC: 7319 AN: 152200 Hom.: 335 Cov.: 32 AF XY: 0.0508 AC XY: 3783 AN XY: 74418

Gnomad4 AFR AF: 0.0760

Gnomad4 AMR AF: 0.0263

Gnomad4 ASJ AF: 0.0337

Gnomad4 EAS AF: 0.197

Gnomad4 SAS AF: 0.167

Gnomad4 FIN AF: 0.0107

Gnomad4 NFE AF: 0.0222

Gnomad4 OTH AF: 0.0482

Alfa AF: 0.0345 Hom.: 25

Bravo AF: 0.0494

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.43

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: rs6714454; hg19: chr2-189291810;