rs7595327

chr2-188434941-G-Achr2-188434941-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.-44-42718G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 151,622 control chromosomes in the GnomAD database, including 7,540 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 0.28 (7540 hom., cov: 32)
• Consequence: GULP1 NM_016315.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0570

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GULP1	NM_016315.4	c.-44-42718G>A		intron_variant		ENST00000409830.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GULP1	ENST00000409830.6	c.-44-42718G>A		intron_variant		1	NM_016315.4	P1

Frequencies

GnomAD3 genomes AF: 0.284 AC: 43062 AN: 151500 Hom.: 7519 Cov.: 32

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.267

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.240

Gnomad NFE AF: 0.199

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.285 AC: 43150 AN: 151622 Hom.: 7540 Cov.: 32 AF XY: 0.282 AC XY: 20874 AN XY: 74100

Gnomad4 AFR AF: 0.502

Gnomad4 AMR AF: 0.195

Gnomad4 ASJ AF: 0.184

Gnomad4 EAS AF: 0.267

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.175

Gnomad4 NFE AF: 0.199

Gnomad4 OTH AF: 0.272

Alfa AF: 0.126 Hom.: 217

Bravo AF: 0.294

Asia WGS AF: 0.285 AC: 984 AN: 3458

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.6
Dann	Benign	0.16

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: rs7595327; hg19: chr2-189299668;