2-188294042-A-G

Variant names:

• chr2-188294042-A-G
• rs6753371
• NM_016315.4:c.-172+1876A>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.-172+1876A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.562 in 152,092 control chromosomes in the GnomAD database, including 24,508 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 0.56 (24498 hom., cov: 33)
  • Exomes 𝑓: 0.60 (10 hom.)
• Consequence: GULP1 NM_016315.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.893
• Publications: 3 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]

LINC01090 (HGNC:49201): (long intergenic non-protein coding RNA 1090)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.874 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GULP1	NM_016315.4	c.-172+1876A>G		intron_variant	Intron 1 of 11	ENST00000409830.6	NP_057399.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GULP1	ENST00000409830.6	c.-172+1876A>G		intron_variant	Intron 1 of 11	1	NM_016315.4	ENSP00000386732.1

Frequencies

GnomAD3 genomes AF: 0.562 AC: 85365 AN: 151922 Hom.: 24500 Cov.: 33

Gnomad AFR AF: 0.554

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.488

Gnomad EAS AF: 0.896

Gnomad SAS AF: 0.633

Gnomad FIN AF: 0.567

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.517

Gnomad OTH AF: 0.587

GnomAD4 exome AF: 0.596 AC: 31 AN: 52 Hom.: 10 Cov.: 0 AF XY: 0.550 AC XY: 22 AN XY: 40

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.750 AC: 3 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.565 AC: 26 AN: 46

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.562 AC: 85407 AN: 152040 Hom.: 24498 Cov.: 33 AF XY: 0.567 AC XY: 42144 AN XY: 74302

African (AFR) AF: 0.554 AC: 22960 AN: 41470

American (AMR) AF: 0.654 AC: 10011 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.488 AC: 1695 AN: 3470

East Asian (EAS) AF: 0.895 AC: 4625 AN: 5166

South Asian (SAS) AF: 0.633 AC: 3052 AN: 4818

European-Finnish (FIN) AF: 0.567 AC: 5976 AN: 10536

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.517 AC: 35150 AN: 67972

Other (OTH) AF: 0.582 AC: 1225 AN: 2106

Alfa AF: 0.532 Hom.: 12768

Bravo AF: 0.574

Asia WGS AF: 0.730 AC: 2537 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	13
DANN	Benign	0.61
PhyloP100		-0.89
PromoterAI		-0.043	Neutral
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: rs6753371; hg19: chr2-189158769;