NM_016315.4:c.*1815T>C

Variant names:

• chr2-188595826-T-C
• rs8273
• NM_016315.4:c.*1815T>C

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_016315.4(GULP1):​c.*1815T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.81 in 152,070 control chromosomes in the GnomAD database, including 51,194 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 0.81 (51022 hom., cov: 32)
  • Exomes 𝑓: 0.89 (172 hom.)
• Consequence: GULP1 NM_016315.4 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.274
• 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 -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.34).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.945 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_016315.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GULP1	NM_016315.4	MANE Select	c.*1815T>C		3_prime_UTR	Exon 12 of 12	NP_057399.1	Q9UBP9-1
	GULP1	NM_001375948.1		c.*1815T>C		3_prime_UTR	Exon 13 of 13	NP_001362877.1	H7BZV7
	GULP1	NM_001375949.1		c.*1815T>C		3_prime_UTR	Exon 14 of 14	NP_001362878.1	H7BZV7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GULP1	ENST00000409830.6	TSL:1 MANE Select	c.*1815T>C		3_prime_UTR	Exon 12 of 12	ENSP00000386732.1	Q9UBP9-1
	GULP1	ENST00000359135.7	TSL:1	c.*1815T>C		3_prime_UTR	Exon 12 of 12	ENSP00000352047.3	Q9UBP9-1
	GULP1	ENST00000908914.1		c.*1815T>C		3_prime_UTR	Exon 13 of 13	ENSP00000578973.1

Frequencies

GnomAD3 genomes AF: 0.810 AC: 122674 AN: 151522 Hom.: 51012 Cov.: 32

Gnomad AFR AF: 0.599

Gnomad AMI AF: 0.950

Gnomad AMR AF: 0.854

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.968

Gnomad FIN AF: 0.904

Gnomad MID AF: 0.921

Gnomad NFE AF: 0.886

Gnomad OTH AF: 0.839

GnomAD4 exome AF: 0.887 AC: 383 AN: 432 Hom.: 172 Cov.: 0 AF XY: 0.888 AC XY: 231 AN XY: 260

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.887 AC: 378 AN: 426

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AF: 1.00 AC: 4 AN: 4

GnomAD4 genome AF: 0.809 AC: 122722 AN: 151638 Hom.: 51022 Cov.: 32 AF XY: 0.813 AC XY: 60230 AN XY: 74108

African (AFR) AF: 0.598 AC: 24776 AN: 41414

American (AMR) AF: 0.854 AC: 12952 AN: 15158

Ashkenazi Jewish (ASJ) AF: 0.844 AC: 2920 AN: 3460

East Asian (EAS) AF: 0.960 AC: 4969 AN: 5176

South Asian (SAS) AF: 0.968 AC: 4666 AN: 4820

European-Finnish (FIN) AF: 0.904 AC: 9575 AN: 10596

Middle Eastern (MID) AF: 0.918 AC: 270 AN: 294

European-Non Finnish (NFE) AF: 0.886 AC: 59957 AN: 67702

Other (OTH) AF: 0.841 AC: 1771 AN: 2106

Alfa AF: 0.856 Hom.: 159203

Bravo AF: 0.794

Asia WGS AF: 0.937 AC: 3244 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.34
CADD	Benign	11
DANN	Benign	0.77
PhyloP100		0.27
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs8273; hg19: chr2-189460553;