chr2-188581744-G-A

Variant names:

• chr2-188581744-G-A
• rs1354905
• NM_016315.4:c.610-2521G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
GULP1	NM_016315.4	c.610-2521G>A		intron_variant	Intron 9 of 11	ENST00000409830.6	NP_057399.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GULP1	ENST00000409830.6	c.610-2521G>A		intron_variant	Intron 9 of 11	1	NM_016315.4	ENSP00000386732.1

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

African (AFR) AF: 0.404 AC: 16740 AN: 41450

American (AMR) AF: 0.523 AC: 7981 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1314 AN: 3470

East Asian (EAS) AF: 0.810 AC: 4188 AN: 5168

South Asian (SAS) AF: 0.650 AC: 3131 AN: 4816

European-Finnish (FIN) AF: 0.486 AC: 5132 AN: 10560

Middle Eastern (MID) AF: 0.483 AC: 142 AN: 294

European-Non Finnish (NFE) AF: 0.446 AC: 30330 AN: 67952

Other (OTH) AF: 0.457 AC: 965 AN: 2112

Alfa AF: 0.454 Hom.: 40250

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
PhyloP100		-0.74
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1354905; hg19: chr2-189446471;