rs1354906

Variant names:

• chr2-188582091-T-C
• rs1354906
• NM_016315.4:c.610-2174T>C

Your query was ambiguous. Multiple possible variants found:

• chr2-188582091-T-C
• chr2-188582091-T-G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_016315.4(GULP1):​c.610-2174T>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
• Publications: 2 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=-0.88).
• 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 rank	MANE	Protein	UniProt
GULP1	NM_016315.4	c.610-2174T>C		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.610-2174T>C		intron_variant	Intron 9 of 11	1	NM_016315.4	ENSP00000386732.1

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

African (AFR) AF: 0.493 AC: 20418 AN: 41386

American (AMR) AF: 0.750 AC: 11452 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.631 AC: 2190 AN: 3470

East Asian (EAS) AF: 0.913 AC: 4690 AN: 5138

South Asian (SAS) AF: 0.800 AC: 3851 AN: 4814

European-Finnish (FIN) AF: 0.776 AC: 8195 AN: 10562

Middle Eastern (MID) AF: 0.784 AC: 229 AN: 292

European-Non Finnish (NFE) AF: 0.698 AC: 47432 AN: 67950

Other (OTH) AF: 0.693 AC: 1463 AN: 2110

Alfa AF: 0.689 Hom.: 18616

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
PhyloP100		-0.75
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: rs1354906; hg19: chr2-189446818;