rs1135850

Variant names:

• chr1-45628020-G-A
• rs1135850
• NM_021639.5:c.*236C>T

Your query was ambiguous. Multiple possible variants found:

• chr1-45628020-G-A
• chr1-45628020-G-C
• chr1-45628020-G-T

Variant summary

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

The NM_021639.5(GPBP1L1):​c.*236C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 464,504 control chromosomes in the GnomAD database, including 19,004 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 (5923 hom., cov: 32)
  • Exomes 𝑓: 0.28 (13081 hom.)
• Consequence: GPBP1L1 NM_021639.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0500
• Publications: 13 publications found

Genes affected

GPBP1L1 (HGNC:28843): (GC-rich promoter binding protein 1 like 1) Predicted to enable DNA binding activity and RNA binding activity. Predicted to be involved in regulation of transcription, DNA-templated. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GPBP1L1	NM_021639.5	c.*236C>T		3_prime_UTR_variant	Exon 13 of 13	ENST00000355105.8	NP_067652.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GPBP1L1	ENST00000355105.8	c.*236C>T		3_prime_UTR_variant	Exon 13 of 13	1	NM_021639.5	ENSP00000347224.3

Frequencies

GnomAD3 genomes AF: 0.276 AC: 41933 AN: 151884 Hom.: 5902 Cov.: 32

Gnomad AFR AF: 0.240

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.288

Gnomad EAS AF: 0.333

Gnomad SAS AF: 0.344

Gnomad FIN AF: 0.219

Gnomad MID AF: 0.326

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.298

GnomAD4 exome AF: 0.281 AC: 87705 AN: 312500 Hom.: 13081 Cov.: 3 AF XY: 0.283 AC XY: 47035 AN XY: 165960

African (AFR) AF: 0.236 AC: 2198 AN: 9300

American (AMR) AF: 0.302 AC: 4168 AN: 13812

Ashkenazi Jewish (ASJ) AF: 0.280 AC: 2640 AN: 9432

East Asian (EAS) AF: 0.291 AC: 5640 AN: 19356

South Asian (SAS) AF: 0.327 AC: 12935 AN: 39556

European-Finnish (FIN) AF: 0.214 AC: 3634 AN: 16994

Middle Eastern (MID) AF: 0.307 AC: 410 AN: 1336

European-Non Finnish (NFE) AF: 0.277 AC: 51139 AN: 184894

Other (OTH) AF: 0.277 AC: 4941 AN: 17820

GnomAD4 genome AF: 0.276 AC: 41993 AN: 152004 Hom.: 5923 Cov.: 32 AF XY: 0.275 AC XY: 20437 AN XY: 74310

African (AFR) AF: 0.240 AC: 9940 AN: 41442

American (AMR) AF: 0.309 AC: 4722 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.288 AC: 999 AN: 3466

East Asian (EAS) AF: 0.333 AC: 1726 AN: 5178

South Asian (SAS) AF: 0.345 AC: 1663 AN: 4824

European-Finnish (FIN) AF: 0.219 AC: 2313 AN: 10548

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19610 AN: 67958

Other (OTH) AF: 0.306 AC: 643 AN: 2104

Alfa AF: 0.266 Hom.: 2434

Bravo AF: 0.281

Asia WGS AF: 0.338 AC: 1177 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.2
DANN	Benign	0.32
PhyloP100		-0.050
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: rs1135850; hg19: chr1-46093692; COSMIC: COSV51974101; COSMIC: COSV51974101;