2-157450699-C-T

Variant names:

• chr2-157450699-C-T
• rs155600
• ENST00000715893.1:c.-91-6693G>A

Variant summary

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

The ENST00000715893.1(CYTIP):​c.-91-6693G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.991 in 152,312 control chromosomes in the GnomAD database, including 74,720 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 0.99 (74720 hom., cov: 31)
• Consequence: CYTIP ENST00000715893.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.310
• Publications: 0 publications found

Genes affected

CYTIP (HGNC:9506): (cytohesin 1 interacting protein) The protein encoded by this gene contains 2 leucine zipper domains and a putative C-terminal nuclear targeting signal, but does not have any hydrophobic regions. This protein is expressed weakly in resting NK and T cells. The encoded protein modulates the activation of ARF genes by CYTH1. This protein interacts with CYTH1 and SNX27 proteins and may act to sequester CYTH1 protein in the cytoplasm.[provided by RefSeq, Aug 2008]

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.985 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CYTIP	ENST00000715893.1	c.-91-6693G>A		intron_variant	Intron 3 of 10			ENSP00000520529.1
CYTIP	ENST00000439355.5	c.-91-6693G>A		intron_variant	Intron 3 of 6	4		ENSP00000402771.1
CYTIP	ENST00000435117.1	c.-91-6693G>A		intron_variant	Intron 4 of 5	3		ENSP00000402155.1
CYTIP	ENST00000497432.5	n.339+14237G>A		intron_variant	Intron 4 of 6	4

Frequencies

GnomAD3 genomes AF: 0.991 AC: 150750 AN: 152194 Hom.: 74663 Cov.: 31

Gnomad AFR AF: 0.984

Gnomad AMI AF: 0.997

Gnomad AMR AF: 0.993

Gnomad ASJ AF: 0.998

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.999

Gnomad FIN AF: 0.997

Gnomad MID AF: 0.984

Gnomad NFE AF: 0.991

Gnomad OTH AF: 0.992

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.991 AC: 150866 AN: 152312 Hom.: 74720 Cov.: 31 AF XY: 0.991 AC XY: 73808 AN XY: 74468

African (AFR) AF: 0.984 AC: 40896 AN: 41568

American (AMR) AF: 0.993 AC: 15202 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.998 AC: 3465 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5194 AN: 5194

South Asian (SAS) AF: 0.999 AC: 4813 AN: 4820

European-Finnish (FIN) AF: 0.997 AC: 10569 AN: 10606

Middle Eastern (MID) AF: 0.983 AC: 289 AN: 294

European-Non Finnish (NFE) AF: 0.991 AC: 67430 AN: 68028

Other (OTH) AF: 0.992 AC: 2099 AN: 2116

Alfa AF: 0.989 Hom.: 27128

Bravo AF: 0.990

Asia WGS AF: 0.999 AC: 3458 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.45
DANN	Benign	0.62
PhyloP100		-0.31
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: rs155600; hg19: chr2-158307211;